Reference change value of global longitudinal strain in clinical practice: A test-rest quality implementation project.

BACKGROUND: Reference change value (RCV) is used to assess the significance of the difference between two measurements after accounting for pre-analytic, analytic, and within-subject variability. The objective of the current study was to define the RCV for global longitudinal strain (GLS) using different semi-automated software in standard clinical practice. METHODS: Using a test-retest study design, we quantified the median coefficient of variation (CV) for GLS using AutoStrain and Automated Cardiac Motion Quantification (aCMQ) by Philips. Triplane left-ventricular ejection fraction (LVEF) was measured for comparison. Multivariable regression analysis was performed to determine factors influencing test-retest CV including image quality and the presence of segmental wall motion abnormalities (WMA). RCV was reported using a standard formula assuming two standard deviations for repeated measurements; results were also translated into Bayesian probability. Total measurement variation was described in terms of its three different components: pre-analytic (acquisition), analytic (measuring variation), and within-subject (biological) variation. RESULT: Of the 44 individuals who were screened, 41 had adequate quality for strain quantification. The mean age of the cohort was 56.4 ± 16.8 years, 41% female, LVEF was 55.8 ± 9.8% and the median and interquartile range for LV GLS was -17.2 [-19.3 to -14.8]%. Autostrain was more time efficient (80% less analysis time) and had a lower total median CV than aCMQ (CV = 7.4% vs. 17.6%, p < .001). The total CV was higher in patients with WMA (6.4% vs. 13.2%, p = .035). In non-segmental disease, the CV translates to a RCV of 15% (corresponding to a probability of real change of 80%). Assuming a within-subject variability of 4.0%, the component analysis identified that inter-reader variability accounts for 3.7% of the CV, while acquisition variability accounts for 4.0%. CONCLUSION: Using test-retest analysis and CVs, we find that an RCV of 15% for GLS represents an optimistic estimate in routine clinical practice. Based on our results, a higher RCV of 17%-21% is needed in order to provide a high probability of clinically meaningful change in GLS in all comers. The methodology presented here for determining measurement reproducibility and RCVs is easily translatable into clinical practice for any imaging parameter.

Is behavioral variation along the bold-shy continuum associated with variation in the stress axis in zebrafish?

We tested whether boldness is associated with attenuation of the physiological stress response in behaviorally selected lines of zebrafish Danio rerio. We measured three component behaviors of boldness: cortisol levels under control and stressed conditions, growth rate, and expression of key genes linked to the hypothalamic-pituitary-interrenal axis in the brain. Surprisingly, bold animals did not differ from shy animals with respect to cortisol levels. However, significant differences between these animals in the expression of glucocorticoid receptors and genes that regulate production of stress hormones indicate that there may still be a relationship between bold behavior and the stress axis. Perhaps the most surprising result of this study was the degree of sexual dimorphism: female zebrafish were bolder than male zebrafish, had significantly lower levels of cortisol, and differed significantly in the expression of several genes in the brain. Our data indicate that a bold behavioral type is associated with transcriptional attenuation of stress axis genes, but we do not yet know whether evolution along the bold-shy continuum is attributable to genetic changes in the stress axis. The bold and shy zebrafish lines will be valuable tools for additional research into the relationship between stress and behavior and the mechanisms regulating sexual dimorphism in these traits.

Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio).

BACKGROUND: Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation. RESULTS: Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer. Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations. Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes. Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4). CONCLUSIONS: Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication. Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication. However, this conclusion must be tempered by limitations associated with comparisons among microarray studies and the low level of population-level replication inherent to these studies.

Non-sex specific genes associated with the secondary mitotic period of primordial germ cell proliferation in the gonads of embryonic rainbow trout (Oncorhynchus mykiss).

The purposes of this study were to quantify the secondary proliferation of primordial germ cells (PGCs) in both sexes of rainbow trout, determine if a sex difference in the timing of PGC proliferation and eventual pre-meiotic number exists, and use microarray data collected during this period to identify genes that are associated with PGC mitosis. The experiments used vasa-green fluorescent protein (vasa-GFP) transgenic rainbow trout of known genetic sex that allowed for the identification and collection of PGCs in vivo. An increase was observed in the number of PGCs counted in the gonads of both female and male embryonic vasa-GFP rainbow trout, from 300 to 700° days (water temperature in °C × days post-fertilization). For both sexes, a statistically significant (P < 0.05) increase in the PGC number was first noted at either 350 or 400° days of development. By 700° days, a 20-50-fold increase in germ cell number was apparent. No sex-specific differences in the timing of PGC proliferation or number were notable in any of the families until 700° days. In conjunction, a custom microarray based on cDNA libraries from embryonic rainbow trout gonads was used to identify genes involved in PGC mitosis. Five genes were discovered: guanine nucleotide binding protein, integral membrane protein 2B, transmembrane protein 47, C-src tyrosine-protein kinase, and the decorin precursor protein. All the genes identified have not been previously associated with germ cell mitosis, but are known to be involved with the cell plasma membrane and/or cell signaling pathways.

Zebrafish (Danio rerio) vary by strain and sex in their behavioral and transcriptional responses to selenium supplementation.

We used the Nadia, Gaighatta, Scientific Hatcheries, and TM1 zebrafish (Danio rerio) strains to test the hypothesis that variation among populations influences the behavioral and transcriptional responses to selenium supplementation. When fed a diet with control levels of selenium, zebrafish strains differed significantly in behavior, characterized as their mean horizontal and vertical swimming positions within the tank. The four strains also differed in brain expression of selenoprotein P1a (sepp1a), glutathione peroxidase 3 (gpx3), thioredoxin reductase 1 (txnrd1), and tRNA selenocysteine associated protein 1 (secp43). Iodothyronine deiodinase 2 (dio2) did not differ among strains but showed a sex-specific expression pattern. When supplemented with selenium, all strains spent a greater proportion of time near the front of the tank, but the response of vertical swimming depth varied by strain. Selenium supplementation also caused changes in selenoprotein expression in the brain that varied by strain for sepp1a, secp43, and dio2, and varied by strain and sex for txnrd1. Expression of gpx3 was unaffected by selenium. Our data indicate that selenium homeostasis in the brain may be a regulator of behavior in zebrafish, and the strain-specific effects of selenium supplementation suggest that genetic heterogeneity among populations can influence the results of selenium supplementation studies.

Dietary carbohydrate level affects transcription factor expression that regulates skeletal muscle myogenesis in rainbow trout.

Understanding the effects of dietary carbohydrates on transcription factors that regulate myogenesis provides insight into the role of nutrient sensing by satellite cells towards myocyte differentiation. We evaluated the influence of dietary carbohydrate level (0, 15, 25 or 35%) on the temporal mRNA expression patterns (4, 8 or 12 weeks) of transcription factors that regulate satellite cell myocyte addition (MA) in rainbow trout (Oncorhynchus mykiss), a vertebrate with indeterminate growth. Relative to the 0% carbohydrate (NC) diet, 15 (IC-15) and 25% (IC-25) carbohydrate containing diets significantly up-regulate MyoD and Myf5, but not Pax7, after 12 weeks of feeding. Simultaneously, the Pax7/MyoD mRNA expression ratio declined significantly with both the IC diets. Myogenin mRNA expression also increased in rainbow trout (RBT) fed the IC-15 diet. The high carbohydrate (HC) diet (35%) attenuated the increased mRNA expression of these transcription factors. It is of note that the 4 and 8 week samples lacked the promyogenic expression patterns. The myogenic gene expression in fish fed the IC-15 diet for 12 weeks indicate a transcriptional signature that reflects increased satellite cell myogenesis. Our results suggest a potential role for satellite cells in the nutrient sensing ability of a vertebrate with indeterminate skeletal muscle growth.

Mapping of five candidate sex-determining loci in rainbow trout (Oncorhynchus mykiss).

BACKGROUND: Rainbow trout have an XX/XY genetic mechanism of sex determination where males are the heterogametic sex. The homology of the sex-determining gene (SDG) in medaka to Dmrt1 suggested that SDGs evolve from downstream genes by gene duplication. Orthologous sequences of the major genes of the mammalian sex determination pathway have been reported in the rainbow trout but the map position for the majority of these genes has not been assigned. RESULTS: Five loci of four candidate genes (Amh, Dax1, Dmrt1 and Sox6) were tested for linkage to the Y chromosome of rainbow trout. We exclude the role of all these loci as candidates for the primary SDG in this species. Sox6i and Sox6ii, duplicated copies of Sox6, mapped to homeologous linkage groups 10 and 18 respectively. Genotyping fishes of the OSU x Arlee mapping family for Sox6i and Sox6ii alleles indicated that Sox6i locus might be deleted in the Arlee lineage. CONCLUSION: Additional candidate genes should be tested for their linkage to the Y chromosome. Mapping data of duplicated Sox6 loci supports previously suggested homeology between linkage groups 10 and 18. Enrichment of the rainbow trout genomic map with known gene markers allows map comparisons with other salmonids. Mapping of candidate sex-determining loci is important for analyses of potential autosomal modifiers of sex-determination in rainbow trout.

Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio).

We used microarray and quantitative real-time PCR (qRT-PCR) analyses in adult female zebrafish (Danio rerio) to identify metabolic pathways regulated by starvation in the liver and brain. The transcriptome of whole zebrafish brain showed little response to 21 days of starvation. Only agouti-related protein 1 (agrp1) significantly responded, with increased expression in brains of starved fish. In contrast, a 21-day period of starvation significantly downregulated 466 and upregulated 108 transcripts in the liver, indicating an overall decrease in metabolic activity, reduced lipid metabolism, protein biosynthesis, proteolysis, and cellular respiration, and increased gluconeogenesis. Starvation also regulated expression of many components of the unfolded protein response, the first such report in a species other than yeast (Saccharomyces cerevisiae) and mice (Mus musculus). The response of the zebrafish hepatic transcriptome to starvation was strikingly similar to that of rainbow trout (Oncorhynchus mykiss) and less similar to mouse, while the response of common carp (Cyprinus carpio) differed considerably from the other three species.

Heat shock protein (HSP70) RNA expression differs among rainbow trout (Oncorhynchus mykiss) clonal lines.

Heat shock protein 70 (HSP70, 70 kDa) is the most commonly expressed protein in response to thermal stress. The extent of its expression is associated with differences in environmental temperatures. We investigated the heat shock response in red blood cells collected from one-year-old rainbow trout (Oncorhynchus mykiss). Three different clonal lines of rainbow trout (Arlee, OSU and Whale Rock) were utilized, originating from habitats that likely experienced different thermal profile. The relative expression of HSP70 from blood cells treated at 13 degrees C, 16 degrees C, 18 degrees C, 20 degrees C, 22 degrees C, and 24 degrees C was quantified using real-time PCR. The use of red blood cells allows for the control and replication of HSP70 expression patterns. Relative expression of HSP70 differed significantly among the three clonal lines. The Arlee line had the lowest HSP70 response of the three clonal lines at any temperature; indicating a heritable difference. Maximum expression of HSP70 occurred at 22 degrees C in the OSU line and at 24 degrees C in the Whale Rock line. The discovery of variation in HSP70 expression among the clonal lines indicates that future studies to map the genetic control of HSP70 expression differences are possible.

Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio).

In this study, we tested for the presence of sexual dimorphism in the hepatic transcriptome of the adult zebrafish and examined the effect of long term manipulation of dietary carbohydrate on gene expression in both sexes. Zebrafish were fed diets comprised of 0%, 15%, 25%, or 35% carbohydrate from the larval stage through sexual maturity, then sampled for hepatic tissue, growth, proximate body composition, and retention efficiencies. Using Affymetrix microarrays and qRT-PCR, we observed substantial sexual dimorphism in the hepatic transcriptome. Males up-regulated genes associated with oxidative metabolism, carbohydrate metabolism, energy production, and amelioration of oxidative stress, while females had higher expression levels of genes associated with translation. Restriction of dietary carbohydrate (0% diet) significantly affected hepatic gene expression, growth performance, retention efficiencies of protein and energy, and percentages of moisture, lipid, and ash. The response of some genes to dietary manipulation varied by sex; with increased dietary carbohydrate, males up-regulated genes associated with oxidative metabolism (e.g. hadhbeta) while females up-regulated genes associated with glucose phosphorylation (e.g. glucokinase). Our data support the use of the zebrafish model for the study of fish nutritional genomics, but highlight the importance of accounting for sexual dimorphism in these studies.

Assignment of rainbow trout linkage groups to specific chromosomes.

The rainbow trout genetic linkage groups have been assigned to specific chromosomes in the OSU (2N=60) strain using fluorescence in situ hybridization (FISH) with BAC probes containing genes mapped to each linkage group. There was a rough correlation between chromosome size and size of the genetic linkage map in centimorgans for the genetic maps based on recombination from the female parent. Chromosome size and structure have a major impact on the female:male recombination ratio, which is much higher (up to 10:1 near the centromeres) on the larger metacentric chromosomes compared to smaller acrocentric chromosomes. Eighty percent of the BAC clones containing duplicate genes mapped to a single chromosomal location, suggesting that diploidization resulted in substantial divergence of intergenic regions. The BAC clones that hybridized to both duplicate loci were usually located in the distal portion of the chromosome. Duplicate genes were almost always found at a similar location on the chromosome arm of two different chromosome pairs, suggesting that most of the chromosome rearrangements following tetraploidization were centric fusions and did not involve homeologous chromosomes. The set of BACs compiled for this research will be especially useful in construction of genome maps and identification of QTL for important traits in other salmonid fishes.

Identification and regulatory analysis of rainbow trout tapasin and tapasin-related genes.

Tapasin (TAPBP) is a key member of MHC class Ia antigen-loading complexes, bridging the class Ia molecule to the transporter associated with antigen presentation (TAP). As part of an ongoing study of MHC genomics in rainbow trout, we have identified two rainbow trout TAPBP genes (Onmy-TAPBP.a and .b) and a similar but distinct TAPBP-related gene (Onmy-TAPBP-R) that had previously only been described in mammals. Physical and genetic mapping indicate that Onmy-TAPBP.a is on chromosome 18 in the MHC class Ia region and that Onmy-TAPBP.b resides on chromosome 14 in the MHC class Ib region. There are also at least two copies of TAPBP-R, Onmy-TAPBP-R.a and Onmy-TAPBP-R.b, located on chromosomes 2 and 3, respectively. Due to the central role of TAPBP expression during acute viral infection, we have characterized the transcriptional profile and regulatory regions for both Onmy-TAPBP and Onmy-TAPBP-R. Transcription of both genes increased during acute infection with infectious hematapoeitic necrosis virus (IHNV) in a fashion indicative of interferon-mediated regulation. Promoter-reporter assays in STE-137 cells demonstrate that the trout TAPBP and TAPBP-R promoters respond to interferon regulatory factors, Onmy-IRF1 and Onmy-IRF2. Overall, TAPBP is expressed at higher levels than TAPBP-R in naïve tissues and TAPBP transcription is more responsive to viral infection and IRF1 and 2 binding.

Intraspecific variation in the rainbow trout mitochondrial DNA genome.

Four complete mitochondrial DNA genomes for rainbow trout, Oncorhynchus mykiss, were sequenced and compared to the previously reported complete mitochondrial sequence. Analyses revealed 13 additional bp and 31 insertion/deletion (indels) sites between the four new sequences and the previously published sequence. Twenty-eight indels were single base pairs while the remaining were multiple base pair insertions, two in the ATPase6 gene, one of three bases and one of nine bases, and a two base insert in the control region. Indels in the new genomes were compared to a wide range of salmonid species and corresponded with sequences in closely related species, indicating that errors were likely incorporated into the previously published sequence. Although variable nucleotide positions were observed throughout the newly sequenced genomes, non-synonymous amino acid substitutions were observed in only six of seven ND genes. While there were only 14 amino acid substitutions between genomes, K(a)/K(s) ratios ranged between 0 and 1. A single amino acid deletion in the ND1 coding region unique to rainbow trout was also detected. Using complete mitochondrial genomes for all sequenced Salmonidae species, a phylogenetic analysis was performed to establish a salmonid mitochondrial phylogeny revealing support for Salvelinus, rather than Salmo, as the sister taxa to Oncorhynchus.

Behavioral differences among rainbow trout clonal lines.

Salmonid fish show considerable geographical variation in morphology, physiology, and behavior. Understanding the genetic mechanisms underlying this variation could be useful for enhancing aquaculture stocks, identifying unique populations for conservation, and determining the genetic factors underlying natural adaptation and domestication. As a first step toward the genetic dissection of salmonid behavioral diversity, we examined variation in behavior patterns among four clonal lines of rainbow trout ( Oncorhynchus mykiss ) derived from geographically diverse source populations with different domestication histories. Clonal lines were crossed with two outbred (i.e., not homozygous) females, and the resulting progenies were reared and tested under identical conditions. Clonal line had significant genetic effects on mean swim level, hiding, foraging, startle response, and aggression level. Multiple comparisons suggest that domestication history of the source populations had a strong influence on these behavior patterns. Progeny of two clonal lines derived from populations reared in captivity for over 100 years exhibited reductions in predator avoidance behavior patterns and increases in aggression compared to progeny of two clonal lines from more recently domesticated populations. These results will facilitate future investigation of the genetic factors underlying population variation in these behavior patterns influenced by domestication.