Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus.

Saprolegnia oomycete infection causes serious economic losses and reduces fish health in aquaculture. Genomic selection based on thousands of DNA markers is a powerful tool to improve fish traits in selective breeding programs. Our goal was to develop a single nucleotide polymorphism (SNP) marker panel and to test its use in genomic selection for improved survival against Saprolegnia infection in European whitefish Coregonus lavaretus, the second most important farmed fish species in Finland. We used a double digest restriction site associated DNA (ddRAD) genotyping by sequencing method to produce a SNP panel, and we tested it analyzing data from a cohort of 1,335 fish, which were measured at different times for mortality to Saprolegnia oomycete infection and weight traits. We calculated the genetic relationship matrix (GRM) from the genome-wide genetic data, integrating it in multivariate mixed models used for the estimation of variance components and genomic breeding values (GEBVs), and to carry out Genome-Wide Association Studies for the presence of quantitative trait loci (QTL) affecting the phenotypes in analysis. We identified one major QTL on chromosome 6 affecting mortality to Saprolegnia infection, explaining 7.7% to 51.3% of genetic variance, and a QTL for weight on chromosome 4, explaining 1.8% to 5.4% of genetic variance. Heritability for mortality was 0.20 to 0.43 on the liability scale, and heritability for weight was 0.44 to 0.53. The QTL for mortality showed an additive allelic effect. We tested whether integrating the QTL for mortality as a fixed factor, together with a new GRM calculated excluding the QTL from the genetic data, would improve the accuracy estimation of GEBVs. This test was done through a cross-validation approach, which indicated that the inclusion of the QTL increased the mean accuracy of the GEBVs by 0.28 points, from 0.33 to 0.61, relative to the use of full GRM only. The area under the curve of the receiver-operator curve for mortality increased from 0.58 to 0.67 when the QTL was included in the model. The inclusion of the QTL as a fixed effect in the model increased the correlation between the GEBVs of early mortality with the late mortality, compared to a model that did not include the QTL. These results validate the usability of the produced SNP panel for genomic selection in European whitefish and highlight the opportunity for modeling QTLs in genomic evaluation of mortality due to Saprolegnia infection.

Saprolegnia infection causes serious economic losses and reduces fish health in aquaculture. We created a novel set of genetic markers to use in the selective breeding of European whitefish to reduce mortality due to the fungus. Using genetic markers, we estimated how much different fish traits are determined by genetic variation, and thus what potential traits have to be selected. We observed that resistance to infection was controlled by both a genetic variant with a major effect on mortality and by many other variants with a small effect distributed across the genome. We tested whether we could increase the precision of genomic breeding values used in the selective breeding by explicitly adding the major genetic variant to the analysis, and we observed an increase in precision in our results. We conclude that directly including information about the major genetic variant increases the precision of our predictions, rather than assuming that all genetic variants each explain a small amount of the genetic variation.

Posterior quadratus lumborum block versus epidural analgesia for postoperative pain management after open radical cystectomy: A randomized clinical trial.

BACKGROUND: In open abdominal surgery, continuous epidural analgesia is commonly used method for postoperative analgesia. However, ultrasound (US)-guided fascial plane blocks may be a reasonable alternative. METHODS: In this randomized controlled trial, we compared posterior quadratus lumborum block (QLB) with epidural analgesia for postoperative pain after open radical cystectomy (ORC). Adult patients aged 18-85 with bladder cancer (BC) scheduled for open RC were randomized in two groups. Exclusion criteria were complicated diabetes mellitus type I, lack of cooperation, and persistent pain for reasons other than BC. In one group, a bilateral US-guided single injection posterior QLB was performed with 3.75 mg/ml ropivacaine 20 ml/side. In the other group, continuous epidural analgesia with ropivacaine was used. Basic analgesia was oral paracetamol 1000 mg three times daily, and long-acting opioid twice daily in both groups. All patients had patient-controlled rescue analgesia with oxycodone. Postoperative cumulative rescue opioid consumption was recorded for the day of surgery, and the following 2 postoperative days (POD 0-2). Secondary outcomes were postoperative pain and nausea and vomiting. RESULTS: In total, 20 patients (QLB), and 19 patients (epidural analgesia) groups, were included in the analyses. Cumulative rescue opioid consumption on POD 0, being of duration 9-12 h, was 14 mg (7.6-33.3) in the QLB group versus 6.1 mg (2.0-16.1) in the epidural analgesia group, p = 0.089, and as doses, 8 doses (3.6-15.7) versus 4 doses (1.3-8.5), p = .057. On POD 1 consumption was 25.3 mg (11.0-52.9) versus 18.0 mg (14.4-43.7), p = .749, and as doses 12 (5.5-23.0) versus 10 (8-20), p > .9, respectively. On POD 2 consumption was 19.1 mg (7.9-31.0) versus 18.0 mg (5.4-27.6) p = .749, and as doses 8.5 (5.2-14.7) versus 11 (3.0-18.0) p > .9, respectively. CONCLUSION: Opioid consumption did not differ significantly between posterior QLB and an epidural infusion with ropivacaine for the first 2 postoperative days following RC. TRIAL REGISTRATION: ClinicalTrials.gov identifier NCT03328988.

Improvement in feed efficiency and reduction in nutrient loading from rainbow trout farms: the role of selective breeding.

Resource efficiency, the ratio of inputs to outputs, is essential for both the economic and environmental performance of any sector of food production. This study quantified the advancement in the feed conversion ratio (FCR) and reduction in nutrient loading from rainbow trout farming in Finland and the degree to which genetic improvements made by a national breeding program have contributed to this advancement. The study combined two datasets. One included annual records on farm-level performance of commercial rainbow trout farms from 1980 onwards, and the other included individuals across eight generations of the national breeding program. The data from the commercial farms showed that from 1980 onwards, the farm-level feed conversion ratio improved by 53.4%, and the specific nitrogen and phosphorus loading from the farms decreased by over 70%. Hence, to produce 1 kg of fish today, only half of the feed is needed compared to the 1980s. The first generation of the breeding program was established in 1992. The FCR was not directly selected for, and hence, the genetic improvement in the FCR is a correlated genetic change in response to the selection for growth and body composition. Since 1992, the estimated genetic improvement in the FCR has been 1.74% per generation, resulting in a cumulative genetic improvement of 11.6% in eight generations. Genetic improvement in the FCR is estimated to be 32.6% of the total improvement in the FCR observed at farms, implying that genetic improvement is a significant contributor to resource efficiency. The use of genetically improved rainbow trout, instead of the base population of fish, reduces feed costs by 18.3% and total production costs by 7.8% at commercial farms (by -0.266€ per kg of ungutted fish). For phosphorus and nitrogen, it can be assumed that the use of fish material with an improved FCR also leads to 18.3% less nitrogen and phosphorus flowing into an aquatic environment. Such improvements in resource efficiency are win-wins for both industry and the environment-the same amount of seafood can be produced with significantly reduced amounts of raw materials and reduced environmental impact.

Resource efficiency, the ratio of inputs to outputs, is essential for both the economic and environmental performance of aquaculture. The data from commercial rainbow trout farms showed that from 1980 onwards, the farm-level feed conversion ratio (FCR) improved by 53.4%, and the specific nitrogen and phosphorus loading from the farms decreased by over 70%. Hence, to produce 1 kg of fish today, only half of the feed is needed compared to the 1980s. Selective breeding is a major contributor to this improvement, and it has resulted in an estimated genetic gain of 1.74% per generation in the FCR. The use of genetically improved rainbow trout, instead of a base population of fish, reduces feed costs and nutrient loading by 18.3% and total production costs by 7.8% at commercial farms. Such improvements in resource efficiency are win­wins for both industry and the environment­the same amount of seafood can be produced with significantly reduced amounts of raw materials and reduced environmental impact.

Conserved QTL and chromosomal inversion affect resistance to columnaris disease in 2 rainbow trout (Oncorhyncus mykiss) populations.

We present a comparative genetic analysis of the quantitative trait loci underlying resistance to warm water columnaris disease in 2 farmed rainbow trout (Oncorhynchus mykiss) populations. We provide evidence for the conservation of a major quantitative trait loci on Omy03, and the putative role played by a chromosomal rearrangement on Omy05. A total of 3,962 individuals from the 2 populations experienced a natural Flavobacterium columnare outbreak. Data for 25,823 genome-wide SNPs were generated for both cases (fatalities) and controls (survivors). FST and pairwise additive genetic relationships suggest that, despite being currently kept as separate broodstocks, the 2 populations are closely related. Association analyses identified a major quantitative trait loci on chromosome Omy03 and a second smaller quantitative trait loci on Omy05. Quantitative trait loci on Omy03 consistently explained 3-11% of genetic variation in both populations, whereas quantitative trait loci on Omy05 showed different degree of association across populations and sexes. The quantitative trait loci on Omy05 was found within a naturally occurring, 54.84 cM long inversion which is easy to tag due to a strong linkage disequilibrium between the 375 tagging SNPs. The ancestral haplotype on Omy05 was associated with decreased mortality. Genetic correlation between mortality in the 2 populations was estimated at 0.64, implying that the genetic basis of resistance is partly similar in the 2 populations. Our quantitative trait loci validation identifies markers that can be potentially used to complement breeding value evaluations to increase resistance against columnaris disease, and help to mitigate effects of climate change on aquaculture.

Ultrasound-guided quadratus lumborum block for postoperative analgesia: A systematic review and meta-analysis.

BACKGROUND: Ultrasound-guided quadratus lumborum block (QLB) is a truncal block with several technique variations. It has been reported as providing effective analgesia for postoperative pain. OBJECTIVES: The aim of this review was to evaluate the efficacy and safety of QLB for postoperative analgesia. The primary outcome was cumulative opioid consumption at 24 h postoperatively. The main secondary outcomes were the time to the first rescue opioid analgesic, pain scores at 24 h postoperatively and the incidence of postoperative nausea and vomiting (PONV). DESIGN: This was a systematic review and meta-analyses of observational studies and randomised controlled trials (RCTs). PRISMA-P guidelines were followed, and the review was registered in PROSPERO. GRADE was used to assess the quality of evidence. DATA SOURCES: The search was performed from several databases (Ovid MEDLINE, PubMed, Scopus, Web of Science, CINAHL and the Cochrane CENTRAL) from inception up to June 2019. ELIGIBILITY CRITERIA: RCTs and prospective observational studies that investigated the postoperative analgesic properties of US-guided single shot QLB in adult patients undergoing abdominal or hip surgery were included. QLB was compared with other analgesics. RESULTS: Twenty-seven studies constituting 1557 patients were reviewed. Twelve studies with 803 patients were included in the meta-analysis on the primary outcome. Overall opioid consumption at 24 h postoperatively was reduced [mean difference, -11.15 (95% CI, -15.33 to -6.97) mg, I2 = 99%, moderate certainty in GRADE] and the time to the first opioid analgesic was longer in patients with QLB: 7 studies with 499 patients, mean difference, 189.32 (95% CI, 114.4 to 264.23) min, I2 = 98%. There were no differences in pain grades. The incidence of PONV was lower in patients with QLB [11 studies with 744 patients, OR 0.40 (95% CI, 0.27 to 0.58), I2 = 7%]. Reported complications and adverse effects of QLB were minimal. CONCLUSION: QLB reduced postoperative opioid consumption, prolonged the time to the first rescue opioid analgesic and diminished the incidence of PONV. QLB appears to be an applicable option for postoperative analgesia after abdominal and hip surgery. REGISTRATION NUMBER: PROSPERO, https://www.crd.york.ac.uk/prospero/, CRD42016039921.

Susceptibility of rainbow trout to three different genogroups of infectious pancreatic necrosis virus.

Infectious pancreatic necrosis (IPN) is a globally distributed viral disease that is highly prevalent in rainbow trout Oncorhynchus mykiss farms in Finland. Seven genogroups (1-7) of infectious pancreatic necrosis virus (IPNV) exist, of which genogroup 5 (serotype Sp) is generally considered to be the most virulent in European salmonid farming. In Finland, 3 genogroups (2, 5 and 6) have been detected. Genogroup 2 is the most widespread and to date is the only genogroup associated with clinical disease in field observations. A bath challenge model infection trial was conducted to investigate the potential pathogenicity of the existing Finnish IPNV genogroups on IPNV-negative rainbow trout fry. Three Finnish IPNV isolates, a positive control (a Norwegian genogroup 5 isolate previously associated with high virulence in Atlantic salmon Salmo salar) and a negative control were used, and mortality was recorded daily for 8 wk. The Finnish IPNV genogroup 5 isolate caused the highest cumulative mortality, and the genogroup 2 isolate also caused elevated mortalities. The genogroup 6 isolate caused only low mortality, and the positive control treatment showed negligible mortality. Fish exposed to the Finnish genogroup 2 and 5 isolates had IPN-associated lesions, while no lesions were noted in the other treatment groups. These results indicate that Finnish IPNV genogroup 5 is potentially the most virulent IPNV genogroup for Finnish rainbow trout. Interestingly, the Norwegian IPNV genogroup 5 isolate caused only a subclinical IPN infection, providing further evidence for a host species-dependent, virus isolate-related difference in virulence in IPNV genogroup 5. The results also support the continuation of legislative disease control of IPNV genogroup 5 in Finnish inland waters.

Sperm pre-fertilization thermal environment shapes offspring phenotype and performance.

The sperm pre-fertilization environment has recently been suggested to mediate remarkable transgenerational consequences for offspring phenotype (transgenerational plasticity, TGB), but the adaptive significance of the process has remained unclear. Here, we studied the transgenerational effects of sperm pre-fertilization thermal environment in a cold-adapted salmonid, the European whitefish (Coregonus lavaretus). We used a full-factorial breeding design where the eggs of five females were fertilized with the milt of 10 males that had been pre-incubated at two different temperatures (3.5°C and 6.5°C) for 15 h prior to fertilization. Thermal manipulation did not affect sperm motility, cell size, fertilization success or embryo mortality. However, offspring that were fertilized with 6.5°C-exposed milt were smaller and had poorer swimming performance than their full-siblings that had been fertilized with the 3.5°C-exposed milt. Furthermore, the effect of milt treatment on embryo mortality varied among different females (treatment×female interaction) and male-female combinations (treatment×female×male interaction). Together, these results indicate that sperm pre-fertilization thermal environment shapes offspring phenotype and post-hatching performance and modifies both the magnitude of female (dam) effects and the compatibility of the gametes. Generally, our results suggest that short-term changes in sperm thermal conditions may have negative impact for offspring fitness. Thus, sperm thermal environment may have an important role in determining the adaptation potential of organisms to climate change. Detailed mechanism(s) behind our findings require further attention.

Thermal sensitivity of growth indicates heritable variation in 1-year-old rainbow trout (Oncorhynchus mykiss).

BACKGROUND: Rainbow trout is an important aquaculture species, which has a worldwide distribution across various production environments. The diverse locations of trout farms involve remarkable variation in environmental factors such as water temperature, which is of major importance for the performance of fish. Thus, robust fish that could thrive under different and suboptimal thermal conditions is a desirable goal for trout breeding. Using a split-family experimental design (40 full-/half-sib groups) for a rainbow trout population derived from the Finnish national breeding program, we studied how two different rearing temperatures (14 and 20 °C) affect feed intake, growth rate and feed conversion ratio in 1-year-old fish. Furthermore, we quantified the additive genetic (co-)variation for daily growth coefficient (DGC) and its thermal sensitivity (TS), defined as the slope of the growth reaction norm between the two temperatures. RESULTS: The fish showed consistently lower feed intake, faster growth and better feed conversion ratio at the lower temperature. Heritability of TS of DGC was moderate ([Formula: see text]). The co-heritability parameter derived from selection index theory, which describes the heritable variance of TS, was negative when the intercept was placed at the lower temperature (-0.28). This resulted in moderate accuracy of selection. At the higher temperature, co-heritability of TS was positive (0.20). The genetic correlation between DGC and its TS was strongly negative (-0.64) when the intercept was at the lower temperature and positive (0.38) but not significantly different from zero at the higher temperature. CONCLUSIONS: The considerable amount of genetic variation in TS of growth indicates a potential for selection response and thus for targeted genetic improvement in TS. The negative genetic correlation between DGC and its TS suggests that selection for high growth rate at the lower temperature will result in more temperature-sensitive fish. Instead, the correlated response of TS is less pronounced if the selection for a higher DGC occurred at the higher temperature. It seems possible to control the correlated genetic change of TS while selecting for fast growth across environments, especially if measurements from both environments are available and breeding values for reaction norm slope are directly included in the selection index.

Genetics of Growth Reaction Norms in Farmed Rainbow Trout.

Rainbow trout is farmed globally under diverse uncontrollable environments. Fish with low macroenvironmental sensitivity (ES) of growth is important to thrive and grow under these uncontrollable environments. The ES may evolve as a correlated response to selection for growth in one environment when the genetic correlation between ES and growth is nonzero. The aims of this study were to quantify additive genetic variance for ES of body weight (BW), defined as the slope of reaction norm across breeding environment (BE) and production environment (PE), and to estimate the genetic correlation (rg(int, sl)) between BW and ES. To estimate heritable variance of ES, the coheritability of ES was derived using selection index theory. The BW records from 43,040 rainbow trout performing either in freshwater or seawater were analysed using a reaction norm model. High additive genetic variance for ES (9584) was observed, inferring that genetic changes in ES can be expected. The coheritability for ES was either -0.06 (intercept at PE) or -0.08 (intercept at BE), suggesting that BW observation in either PE or BE results in low accuracy of selection for ES. Yet, the rg(int, sl) was negative (-0.41 to -0.33) indicating that selection for BW in one environment is expected to result in more sensitive fish. To avoid an increase of ES while selecting for BW, it is possible to have equal genetic gain in BW in both environments so that ES is maintained stable.

Genetic (co)variance of rainbow trout (Oncorhynchus mykiss) body weight and its uniformity across production environments.

BACKGROUND: When rainbow trout from a single breeding program are introduced into various production environments, genotype-by-environment (GxE) interaction may occur. Although growth and its uniformity are two of the most important traits for trout producers worldwide, GxE interaction on uniformity of growth has not been studied. Our objectives were to quantify the genetic variance in body weight (BW) and its uniformity and the genetic correlation (rg) between these traits, and to investigate the degree of GxE interaction on uniformity of BW in breeding (BE) and production (PE) environments using double hierarchical generalized linear models. Log-transformed data were also used to investigate whether the genetic variance in uniformity of BW, GxE interaction on uniformity of BW, and rg between BW and its uniformity were influenced by a scale effect. RESULTS: Although heritability estimates for uniformity of BW were low and of similar magnitude in BE (0.014) and PE (0.012), the corresponding coefficients of genetic variation reached 19 and 21%, which indicated a high potential for response to selection. The genetic re-ranking for uniformity of BW (rg = 0.56) between BE and PE was moderate but greater after log-transformation, as expressed by the low rg (-0.08) between uniformity in BE and PE, which indicated independent genetic rankings for uniformity in the two environments when the scale effect was accounted for. The rg between BW and its uniformity were 0.30 for BE and 0.79 for PE but with log-transformed BW, these values switched to -0.83 and -0.62, respectively. CONCLUSIONS: Genetic variance exists for uniformity of BW in both environments but its low heritability implies that a large number of relatives are needed to reach even moderate accuracy of selection. GxE interaction on uniformity is present for both environments and sib-testing in PE is recommended when the aim is to improve uniformity across environments. Positive and negative rg between BW and its uniformity estimated with original and log-transformed BW data, respectively, indicate that increased BW is genetically associated with increased variance in BW but with a decrease in the coefficient of variation. Thus, the scale effect substantially influences the genetic parameters of uniformity, especially the sign and magnitude of its rg.

Untangling the positive genetic correlation between rainbow trout growth and survival.

Explanations for positive and negative genetic correlations between growth and fitness traits are essential for life-history theory and selective breeding. Here, we test whether growth and survival display genetic trade-off. Furthermore, we assess the potential of third-party traits to explain observed genetic associations. First, we estimated genetic correlations of growth and survival of rainbow trout. We then explored whether these associations are explained by genetic correlations with health, body composition and maturity traits. Analysis included 14 traits across life stages and environments. Data were recorded from 249 166 individuals belonging to 10 year classes of a pedigreed population. The results revealed that rapid growth during grow-out was genetically associated with enhanced survival (mean r(G) = 0.17). This resulted because genotypes with less nematode caused cataract grew faster and were more likely to survive. Fingerling survival was not genetically related to weight or to grow-out survival. Instead, rapid fingerling growth made fish prone to deformations (r(G) = 0.18). Evolutionary genetics provides a theoretical framework to study variation in genetic correlations. This study demonstrates that genetic correlation patterns of growth and survival can be explained by a set of key explanatory traits recorded at different life stages and that these traits can be simultaneously improved by selective breeding.

Genetic architecture of rainbow trout survival from egg to adult.

Survival from birth to a reproductive adult is a challenge that only robust individuals resistant to a variety of mortality factors will overcome. To assess whether survival traits share genetic architecture throughout the life cycle, we estimated genetic correlations for survival within fingerling stage, and across egg, fingerling and grow-out stages in farmed rainbow trout. Genetic parameters of survival at three life cycle stages were estimated for 249 166 individuals originating from ten year classes of a pedigreed population. Despite being an important fitness component, survival traits harboured significant but modest amount of genetic variation (h2=0.07-0.27). Weak associations between survival during egg-fry and fingerling periods, between early and late fingerling periods (rG=0.30) and generally low genetic correlations between fingerling and grow-out survival (mean rG=0.06) suggested that life-stage specific survival traits are best regarded as separate traits. However, in the sub-set of data with detailed time of death records, positive genetic correlations between early and late fingerling survival (rG=0.89) showed that during certain years the best genotypes in the early period were also among the best in the late period. That survival across fingerling period can be genetically the same, trait was indicated also by only slightly higher heritability (h2=0.15) estimated with the survival analysis of time to death during fingerling period compared to the analysis treating fingerling survival as a binary character (h2=0.11). The results imply that (1) inherited resistance against unknown mortality factors exists, but (2) ranking of genotypes changes across life stages.

Serum growth factors in asbestosis patients.

Various growth factors, including platelet-derived growth factor (PDGF) and transforming growth factor (TGF)-beta, have been implicated in the pathogenesis of asbestos-induced disease. PDGF and TGF-beta levels were determined by enzyme-linked immunosorbent assays in the banked serum samples of a cohort of workers with asbestosis, and the relationships of the growth factor levels to the subsequent development of cancer and to the radiographic severity and progression of asbestosis in the cohort were examined. Serum levels of PDGF and TGF-beta were found to be unrelated to the development of cancer, and serum levels of PDGF were found to be unrelated to the severity and progression of asbestosis. However, serum levels of TGF-beta were found to be statistically significantly related to disease severity (p = 0.01), increasing approximately 2.4-fold from ILO radiographic category 0 to category 3, and they were marginally related to disease progression (p = 0.07), in multivariate analysis controlling for other contributory factors including cumulative asbestos exposure. This suggests that serum TGF-beta may be a useful biomarker for asbestos-induced fibrotic disease.

Survival of the currently fittest: genetics of rainbow trout survival across time and space.

As a fitness trait, survival is assumed to exhibit low heritability due to strong selection eroding genetic variation and/or spatio-temporal variation in mortality agents reducing genetic and increasing residual variation. The latter phenomenon in particular may contribute to low heritability in multigeneration data, even if certain cohorts exhibit significant genetic variation. Analysis of survival data from 10 year classes of rainbow trout reared at three test stations showed that treating survival as a single trait across all generations resulted in low heritability (h2 = 0.08-0.17). However, when heritabilities were estimated from homogeneous generation and test station-specific cohorts, a wide range of heritability values was revealed (h2 = 0.04-0.71). Of 64 genetic correlations between different cohorts, 20 were positive, but 16 were significantly negative, confirming that genetic architecture of survival is not stable across generations and environments. These results reveal the existence of hidden genetic variation for survival and demonstrate that treating survival as one trait over several generations may not reveal its true genetic architecture. Negative genetic correlations between cohorts indicate that overall survival has limited potential to predict general resistance, and care should be taken when using it as selection criterion.

Developmental disturbances in early life stage mortality (M74) of Baltic salmon fry as studied by changes in gene expression.

BACKGROUND: We have studied alterations of gene expression associated with naturally-occurring early life stage mortality (M74) in Baltic salmon using a cDNA microarray and real time PCR. M74-affected fry have several typical neurological, cardiovascular and pathological symptoms. They are also characterized by low thiamine content and show signs of oxidative stress. RESULTS: Affected fry can be divided into three major groups with early, intermediate or late onset of mortality. If mortality starts during the first third of the yolk-sac stage, virtually all the responses are compatible with stress, which rapidly leads to the common terminal responses. If death occurs during the second third of the yolk sac stage, the terminal stage is preceded by a decrease in globin gene expression, which leads to internal hypoxia when the animals grow and shift from skin- to gill-breathing. Fry will eventually proceed to the terminal responses. The group developing M74 most slowly appears to compensate for reduced oxygen delivery by downregulation of metabolism, and hence some fry can escape death. CONCLUSION: Our study is the first demonstration of diverse transcriptional responses to a naturally-occurring developmental disturbance. Since many of the genes differentially expressed in M74-fry are evolutionarily conserved, the M74 of Baltic salmon can serve as a model for developmental disturbances and environmental stress responses in vertebrates in general.

Transcribed Tc1-like transposons in salmonid fish.

BACKGROUND: Mobile genetic elements comprise a substantial fraction of vertebrate genomes. These genes are considered to be deleterious, and in vertebrates they are usually inactive. High throughput sequencing of salmonid fish cDNA libraries has revealed a large number of transposons, which remain transcribed despite inactivation of translation. This article reports on the structure and potential role of these genes. RESULTS: A search of EST showed the ratio of transcribed transposons in salmonid fish (i.e., 0.5% of all unique cDNA sequences) to be 2.4-32 times greater than in other vertebrate species, and 68% of these genes belonged to the Tc1-family of DNA transposons. A phylogenetic analysis of reading frames indicate repeated transposition of distantly related genes into the fish genome over protracted intervals of evolutionary time. Several copies of two new DNA transposons were cloned. These copies showed relatively little divergence (11.4% and 1.9%). The latter gene was transcribed at a high level in rainbow trout tissues, and was present in genomes of many phylogenetically remote fish species. A comparison of synonymous and non-synonymous divergence revealed remnants of divergent evolution in the younger gene, while the older gene evolved in a neutral mode. From a 1.2 MB fragment of genomic DNA, the salmonid genome contains approximately 10(5) Tc1-like sequences, the major fraction of which is not transcribed. Our microarray studies showed that transcription of rainbow trout transposons is activated by external stimuli, such as toxicity, stress and bacterial antigens. The expression profiles of Tc1-like transposons gave a strong correlation (r2 = 0.63-0.88) with a group of genes implicated in defense response, signal transduction and regulation of transcription. CONCLUSION: Salmonid genomes contain a large quantity of transcribed mobile genetic elements. Divergent or neutral evolution within genomes and lateral transmission can account for the diversity and sustained persistence of Tc1-like transposons in lower vertebrates. A small part of transposons remain transcribed and their transcription is enhanced by responses to acute conditions.

Steady-state effects of temperature acclimation on the transcriptome of the rainbow trout heart.

Cold-acclimated (CA) phenotype of trout heart was induced by 4-wk acclimation at 4 degrees C and was characterized by 32.7% increase in relative heart mass and 49.8% increase in ventricular myocyte size compared with warm-acclimated (WA; 18 degrees C) fish (P < 0.001). Effect of temperature acclimation on transcriptome of the rainbow trout heart was examined using species-specific microarray chips containing 1,380 genes. After 4 wk of temperature acclimation, 8.8% (122) of the genes were differently expressed in CA and WA hearts, and most of them (82%) were upregulated in the cold (P < 0.01). Transcripts of genes engaged in protein synthesis and intermediary metabolism were most strongly upregulated, whereas genes contributing to the connective tissue matrix were clearly repressed. Extensive upregulation of the genes coding for ribosomal proteins and translation elongation and initiation factors suggest that the protein synthesis machinery of the trout heart is enhanced in the cold and is an essential part of the compensatory mechanism causing and maintaining the hypertrophy of cardiac myocytes. The prominent depression of collagen genes may be indicative of a reduced contribution of extracellular matrix to the remodeling of the CA fish heart. Temperature-related changes in transcripts of metabolic enzymes suggest that at mRNA level, glycolytic energy production from carbohydrates is compensated in the heart of CA rainbow trout, while metabolic compensation is absent in mitochondria. In addition, the analysis revealed three candidate genes: muscle LIM protein, atrial natriuretic peptide B, and myosin light chain 2, which might be central for induction and maintenance of the hypertrophic phenotype of the CA trout heart. These findings indicate that extensive modification of gene expression is needed to maintain the temperature-specific phenotype of the fish heart.

Transcriptome responses to carbon tetrachloride and pyrene in the kidney and liver of juvenile rainbow trout (Oncorhynchus mykiss).

We report the effects of the hepatotoxic compound carbon tetrachloride (CCl(4)) and pyrene, a model polycyclic aromatic hydrocarbon, on the transcriptomes of juvenile rainbow trout kidneys and livers. Fish were exposed to sublethal doses for 4 days and expression of 1273 genes was measured using a cDNA microarray. Efforts were focused on differentiating between unspecific responses and those that can be regarded as molecular signatures of CCl(4) and pyrene toxicities. Expression profiles were analyzed in terms of Gene Ontology categories. Universal reactions to chemical toxicity were observed in metallothionein, HSP90 and mitochondrial proteins of oxidative phosphorylation, which were induced in both tissues. Several genes showed similar responses to both compounds in either kidney or liver; most of the effects are implicated in hematopoiesis and immune response. Stimulation of mitochondrial and heat shock proteins was greater in the liver than in the kidney, whereas genes involved in transcription, humoral immune response and apoptosis were suppressed. Pyrene and CCl(4) caused opposite effects on expression of several genes, including HSP-27, macrophage receptor Marco, metalloproteinases (MMP9 and MMP13), and delta-6 fatty acid desaturase. Pyrene affected mainly genes implicated in the maintenance of the genetic apparatus, immune response, glycolysis, and iron homeostasis. CCl(4) affected the structural proteins and genes involved in cellular stress, protein folding, and steroid metabolism. Overall, pyrene suppressed a range of protective or acclimative reactions, many of which were stimulated with CCl(4). Additionally, gene profiling analyses indicated adaptive and potentially maladaptive reactions to toxicity. For instance, stimulation of mitochondrial proteins coincided with suppression of catalase, whereas CCl(4) down-regulated fatty acid metabolism and peroxisomal proteins. A number of candidate biomarkers for ecotoxicological risk assessment were identified as our understanding of mechanisms of pyrene and CCl(4) toxicities in rainbow trout increased.

Impairment of lung function in asbestos-exposed workers in relation to high-resolution computed tomography.

OBJECTIVES: The aim of the study was to determine the causes of impairment of ventilatory function and diffusing capacity in smoking asbestos-exposed workers (N=590) showing radiological pleural thickenings or pulmonary fibrosis. METHODS: High-resolution computed tomography (HRCT) and spirometry were performed, and diffusing capacity was measured. The workers were divided into five groups based on the HRCT scoring: pleural disease (N=190), pulmonary fibrosis (N=68), emphysema (N=148), combined fibrosis and emphysema (N=74), and marked adhesions (N=110). The graded lung function impairment was compared between the groups. RESULTS: Moderate impairment of forced expiratory volume in 1 second [odds ratio (OR) 2.72, 95% confidence interval (95% CI) 1.31-5.57] and forced vital capacity (OR 2.81, 95% CI 1.05-6.89) was associated with the persons with combined fibrosis and emphysema. Marked impairment of diffusing capacity was associated with the combined fibrosis and emphysema (OR 4.94, 95% CI 2.48-9.77) but not with pleural disease (OR 0.21, 95% CI 0.09-0.45) or pulmonary fibrosis (OR 0.36, 95% CI 0.08-1.05). For the persons with combined fibrosis and emphysema, the mean fibrosis score did not differ between normal, slightly reduced, or markedly reduced diffusing capacity, but the emphysema score was significantly higher for the patients with marked impairment than for those with normal diffusing capacity (P < 0.01). CONCLUSIONS: Different profiles of asbestos- and smoking-induced pulmonary or pleural disease were found. The results indicate that the most important factor determining the degree of functional impairment in smoking asbestos-exposed workers is the presence of pulmonary emphysema.

Gene expression in the brain and kidney of rainbow trout in response to handling stress.

BACKGROUND: Microarray technologies are rapidly becoming available for new species including teleost fishes. We constructed a rainbow trout cDNA microarray targeted at the identification of genes which are differentially expressed in response to environmental stressors. This platform included clones from normalized and subtracted libraries and genes selected through functional annotation. Present study focused on time-course comparisons of stress responses in the brain and kidney and the identification of a set of genes which are diagnostic for stress response. RESULTS: Fish were stressed with handling and samples were collected 1, 3 and 5 days after the first exposure. Gene expression profiles were analysed in terms of Gene Ontology categories. Stress affected different functional groups of genes in the tissues studied. Mitochondria, extracellular matrix and endopeptidases (especially collagenases) were the major targets in kidney. Stress response in brain was characterized with dramatic temporal alterations. Metal ion binding proteins, glycolytic enzymes and motor proteins were induced transiently, whereas expression of genes involved in stress and immune response, cell proliferation and growth, signal transduction and apoptosis, protein biosynthesis and folding changed in a reciprocal fashion. Despite dramatic difference between tissues and time-points, we were able to identify a group of 48 genes that showed strong correlation of expression profiles (Pearson r > /0.65/) in 35 microarray experiments being regulated by stress. We evaluated performance of the clone sets used for preparation of microarray. Overall, the number of differentially expressed genes was markedly higher in EST than in genes selected through Gene Ontology annotations, however 63% of stress-responsive genes were from this group. CONCLUSIONS: 1. Stress responses in fish brain and kidney are different in function and time-course. 2. Identification of stress-regulated genes provides the possibility for measuring stress responses in various conditions and further search for the functionally related genes.