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ABSTRACT: High-throughput microarray experiments often generate far more biological information than is required to test the experimental hypotheses. Many microarray analyses are considered finished after differential expression and additional analyses are typically not performed, leaving untapped biological information left undiscovered. This is especially true if the microarray experiment is from an ecological study of multiple populations. Comparisons across populations may also contain important genomic polymorphisms, and a subset of these polymorphisms may be identified with microarrays using techniques for the detection of single feature polymorphisms (SFP). SFPs are differences in microarray probe level intensities caused by genetic polymorphisms such as single-nucleotide polymorphisms and small insertions/deletions and not expression differences. In this study, we provide a new algorithm for the detection of SFPs, evaluate the algorithm using existing data from two publicly available Affymetrix Barley (Hordeum vulgare) microarray data sets and compare them to two previously published SFP detection algorithms. Results show that our algorithm provides more consistent and sensitive calling of SFPs with a lower false discovery rate. Simultaneous analysis of SFPs and differential expression is a low-cost method for the enhanced analysis of microarray data, enabling additional biological inferences to be made.
Molecular Ecology Resources 09/2012; 12(6):1079-89. · 3.06 Impact Factor
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ABSTRACT: 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.
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).
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.
BMC Genomics 07/2012; 13:323. · 4.07 Impact Factor
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ABSTRACT: Because early social experience can have a profound effect on later mate and social choices, the availability of options and
decisions made early in development can have major effects on adult behavior. Herein, we use strain differences among zebrafish,
Danio rerio, as an experimental tool to test the effects of social experience on behavior. By manipulating the strain composition of
groups in which the subject fish are housed at different ages, we tested (1) whether mixing with dissimilar individuals influenced
subsequent behavior, (2) whether prolonged mixing during the juvenile stage had a more pronounced effect than a shorter period
of mixing during adulthood and (3) whether mixing had a lasting effect after animals were resorted into groups of same strain
animals. We found that social experience had a profound impact on social behavior. Both Nadia and TM1 individuals engaged
in more frequent biting after having been in mixed strain groups compared to pure strain groups. This was true of groups mixed
as juveniles, as well as adults, indicating that this response was not dependent on exposure during a critical developmental
period. Also, TM1 fish (but not Nadia) having recently been housed in mixed-strain groups were more willing to leave the immediate
vicinity of a shoal than were TM1 fish raised in pure strain groups. This change was more pronounced in groups mixed as juveniles
than as adults. In addition, the observed changes persisted after mixed groups were separated into pure strain groups for
a month. Other behavioral measures including Activity Level, Predator Response and Stress Recovery were unaffected by previous
social experience.
Environmental Biology of Fishes 04/2012; 80(1):91-101. · 0.91 Impact Factor
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11/2011: pages 55 - 67; , ISBN: 9780470963159
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ABSTRACT: The zebrafish retina regenerates in response to acute retinal lesions, replacing damaged neurons with new neurons. In this study we test the hypothesis that chronic stress to inner retinal neurons also triggers a retinal regeneration response in the bugeye zebrafish. Mutations in the lrp2 gene in zebrafish are associated with a progressive eye phenotype (bugeye) that models several risk factors for human glaucoma including buphthalmos (enlarged eyes), elevated intraocular pressure (IOP), and upregulation of genes related to retinal ganglion cell pathology. The retinas of adult bugeye zebrafish showed high rates of ongoing proliferation which resulted in the production of a small number of new retinal neurons, particularly photoreceptors. A marker of mechanical cell stress, Hsp27, was strongly expressed in inner retinal neurons and glia of bugeye retinas. The more enlarged eyes of individual bugeye zebrafish showed disrupted retinal lamination, and a persistent reduced density of neurons in the ganglion cell layer (GCL), although total numbers of GCL neurons were higher than in control eyes. Despite the presence of a proliferative response to damage, the adult bugeye zebrafish remained behaviorally blind. These findings suggest the existence of an unsuccessful regenerative response to a persistent pathological condition in the bugeye zebrafish.
Experimental Eye Research 06/2011; 93(4):424-36. · 3.26 Impact Factor
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ABSTRACT: The study was designed to test the hypothesis that male aging is associated with a change in reproductive function in the zebrafish. Young (290 ± 37 d) and older (911 ± 48 d) males were combined with females (604 ± 24 d) to test the effect of male age on the number and fertility of eggs laid by their mates. 48% of breeding trials with young males and 25% of the trails with older males resulted in egg deposition. Although young males were associated with significantly more successful breeding attempts than older males, number of eggs laid per clutch, number and percent of fertilized eggs and the number and percent living embryos were not statistically different between young and older males. These data suggest that male aging is associated with altered reproductive behavior and/or female response but not in sperm quality per se. Consistent with this interpretation were the findings that percent motility and sperm motility characteristics did not differ between sperm from young and older males as assessed by computer-assisted sperm analysis. However, older males contained higher quantities of extractable sperm than did young males, perhaps associated with fewer successful breeding attempts. Age-related effects on male reproductive in the zebrafish may therefore be a consequence of behavioral or morphological features that play a role in female mate choice and/ or male sexual response.
Journal of Experimental Zoology Part A Ecological Genetics and Physiology 03/2011; 315(3):156-61. · 1.64 Impact Factor
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ABSTRACT: 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.
Comparative biochemistry and physiology. Part A, Molecular & integrative physiology 12/2010; 157(4):310-8. · 2.20 Impact Factor
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ABSTRACT: 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.
Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 02/2009; 153(1):66-72. · 1.61 Impact Factor
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ABSTRACT: 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.
Physiological Genomics 09/2008; 35(3):283-95. · 2.73 Impact Factor
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Barrie D Robison,
Robert E Drew,
Gordon K Murdoch,
Madison Powell,
Kenneth J Rodnick,
Matt Settles,
David Stone,
Erin Churchill,
Rodney A Hill,
Madhusudhan R Papasani,
Solange S Lewis,
Ronald W Hardy
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ABSTRACT: 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.
Comparative Biochemistry and Physiology Part D Genomics and Proteomics 06/2008; 3(2):141-54. · 1.72 Impact Factor
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ABSTRACT: Studies of "behavioral syndromes" in different populations and species of animals can be used to shed light on the underlying mechanisms of evolution. For example, some personality syndromes suggest the existence of an underlying hormonal link, whereas other relationships between boldness and aggression appear to be the result of similar selective pressures. Here, we used 1 wild-derived and 2 laboratory strains of zebrafish (Danio rerio) to examine relationships among 5 behavioral measures: shoaling, activity level, predator approaches, latency to feed after a disturbance, and biting to a mirror stimulus. We found evidence of an activity syndrome, as if underlying metabolic costs influence variation in multiple forms of behavior. Evidence for a relationship between boldness and aggression was also apparent but depended both on strain and which specific behavior patterns were identified as measures of "boldness." Although some comparisons of laboratory and wild-derived strains were consistent with a domestication syndrome, others were not. Most observed relationships were relatively weak and occasionally inconsistent, arguing against strong underlying genetic linkages or pleiotropic effects relating any of the behavioral measures. Instead, it may be more important to study the details of selective context or the long-term impact of linkages between some, but not all, of a large set of genes influencing complex behavioral traits. We found profound differences among strains in most behavior patterns, but few sex differences. One strain (TM1) was consistently different from the others (SH and Nadia) being more social, more likely to approach predators, and taking less time to recover from disturbance than were the other 2 strains. Copyright 2007, Oxford University Press.
Behavioral Ecology. 01/2007; 18(3):556-562.
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ABSTRACT: We have cloned a second insulin gene in zebrafish and studied temporal and spatial expression of two zebrafish insulin genes. Zebrafish insulin-a (insa) and -b (insb) mRNAs are derived from two different DNA contigs on chromosomes 5 and 14, respectively, representing two different insulin genes. Real-time PCR studies suggest that insa is a maternal and also a postzygotic transcript. insa was observed at 1 h postfertilization (hpf) and was rapidly degraded by 6 and 12 hpf but induced at 24 hpf (i.e., after pancreas formation). Expression levels at 24 hpf were approximately 220-fold higher than at 6 hpf and were significantly different from earlier time points. At 72 hpf (at time of hatching), zebrafish insa mRNA levels tended to be higher than at 24 hpf and were approximately 727-fold higher compared with 6 hpf. This further increase in insa expression may be one of the many rapid physiological changes associated with hatching. insb expression was observed from 1 hpf and was significantly decreased from 12 hpf onward. Its expression levels at 12 and 24 hpf were approximately twofold and sixfold lower, respectively, compared with expression at 6 hpf. insb expression levels at 48 hpf were significantly lower than at 24 hpf but not different from 72 hpf. Expression levels at 72 hpf were approximately 61-fold lower than at 6 hpf. In situ hybridization studies showed insb expression in proliferating blastomeres at 3 and 4 hpf. At later time points, insb expression was restricted to the brain and pancreas (24 and 48 hpf). insa expression was observed in the pancreas at 24 and 48 hpf. Expression of insb in blastomeres and head suggests that insb could be acting as a pro-growth, survival, and neurotrophic factor during development. Pancreatic insa and insb may both be involved in regulation of glucose homeostasis as in mammals.
Physiological Genomics 11/2006; 27(1):79-85. · 2.73 Impact Factor
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Gary H Thorgaard,
George S Bailey,
David Williams,
Donald R Buhler,
Stephen L Kaattari,
Sandra S Ristow,
John D Hansen,
James R Winton,
Jerri L Bartholomew,
James J Nagler,
Patrick J Walsh,
Matt M Vijayan,
Robert H Devlin,
Ronald W Hardy,
Kenneth E Overturf,
William P Young, Barrie D Robison,
Caird Rexroad,
Yniv Palti
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ABSTRACT: The rainbow trout (Oncorhynchus mykiss) is one of the most widely studied of model fish species. Extensive basic biological information has been collected for this species, which because of their large size relative to other model fish species are particularly suitable for studies requiring ample quantities of specific cells and tissue types. Rainbow trout have been widely utilized for research in carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. They are distinctive in having evolved from a relatively recent tetraploid event, resulting in a high incidence of duplicated genes. Natural populations are available and have been well characterized for chromosomal, protein, molecular and quantitative genetic variation. Their ease of culture, and experimental and aquacultural significance has led to the development of clonal lines and the widespread application of transgenic technology to this species. Numerous microsatellites have been isolated and two relatively detailed genetic maps have been developed. Extensive sequencing of expressed sequence tags has begun and four BAC libraries have been developed. The development and analysis of additional genomic sequence data will provide distinctive opportunities to address problems in areas such as evolution of the immune system and duplicate genes.
Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology 01/2003; 133(4):609-46. · 1.92 Impact Factor
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ABSTRACT: Abstract 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.
Physiological and Biochemical Zoology 85(6):718-28. · 2.20 Impact Factor
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ABSTRACT: The genetic basis of development rate was examined using clonal lines of rainbow trout produced by androgenesis. We examined development rate, as indicated by physiological time to hatch (°days), of four clonal lines of rainbow trout crossed to outbred females in three separate experiments. In the first experiment, the Swanson line, derived from an Alaskan population, displayed a significantly earlier physiological time to hatch than the Arlee line, derived from a domesticated rainbow trout (P<0.001). In the second experiment, this trend was maintained across three temperatures (approximately 8, 10, and 14°C) and two females, although the experiment lacked the statistical power to detect a difference (P=0.052). In the third experiment, the Swanson line had a significantly earlier physiological time to hatch than three other clonal lines (P<0.01) when tested across three temperatures (8, 10, and 16°C) and two females. There was no evidence of genotype by environment interaction in any of the experiments. These data indicate that development rate has a strong genetic component, and that the clonal lines of rainbow trout available should be highly suitable for QTL analysis of development rate in rainbow trout.
Aquaculture.
