Journal articles on the topic 'Fish Physiology and Genetics'
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1
Lu, Yingchang, Mark V. Boekschoten, Suzan Wopereis, Michael Müller, and Sander Kersten. "Comparative transcriptomic and metabolomic analysis of fenofibrate and fish oil treatments in mice." Physiological Genomics 43, no. 23 (December 2011): 1307–18. http://dx.doi.org/10.1152/physiolgenomics.00100.2011.
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Elevated circulating triglycerides, which are considered a risk factor for cardiovascular disease, can be targeted by treatment with fenofibrate or fish oil. To gain insight into underlying mechanisms, we carried out a comparative transcriptomics and metabolomics analysis of the effect of 2 wk treatment with fenofibrate and fish oil in mice. Plasma triglycerides were significantly decreased by fenofibrate (−49.1%) and fish oil (−21.8%), whereas plasma cholesterol was increased by fenofibrate (+29.9%) and decreased by fish oil (−32.8%). Levels of various phospholipid species were specifically decreased by fish oil, while levels of Krebs cycle intermediates were increased specifically by fenofibrate. Plasma levels of many amino acids were altered by fenofibrate and to a lesser extent by fish oil. Both fenofibrate and fish oil upregulated genes involved in fatty acid metabolism and downregulated genes involved in blood coagulation and fibrinolysis. Significant overlap in gene regulation by fenofibrate and fish oil was observed, reflecting their property as high or low affinity agonist for peroxisome proliferator-activated receptor-α, respectively. Fenofibrate specifically downregulated genes involved in complement cascade and inflammatory response. Fish oil specifically downregulated genes involved in cholesterol and fatty acid biosynthesis and upregulated genes involved in amino acid and arachidonic acid metabolism. Taken together, the data indicate that despite being similarly potent toward modulating plasma free fatty acids, cholesterol, and triglyceride levels, fish oil causes modest changes in gene expression likely via activation of multiple mechanistic pathways, whereas fenofibrate causes pronounced gene expression changes via a single pathway, reflecting the key difference between nutritional and pharmacological intervention.
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Oliveira, C., F. Foresti, and A. W. S. Hilsdorf. "Genetics of neotropical fish: from chromosomes to populations." Fish Physiology and Biochemistry 35, no. 1 (August 6, 2008): 81–100. http://dx.doi.org/10.1007/s10695-008-9250-1.
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Grønkjær, Peter. "Otoliths as individual indicators: a reappraisal of the link between fish physiology and otolith characteristics." Marine and Freshwater Research 67, no. 7 (2016): 881. http://dx.doi.org/10.1071/mf15155.
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Otoliths are remarkable recorders that store visual and chemical information that can be interpreted with regard to individual fish phenotype trajectory, life history events and environment. However, the information stored in the otoliths must be interpreted with the knowledge that the otolith is an integral part of fish sensory systems. This means that the environmental signals recorded in the otoliths will be regulated by the homeostatic apparatus of the individual fish – its physiology and ultimately its genetic make-up. Although this may complicate interpretation of environmental signals, it also opens up avenues for new research into the physiology and life history of individual fish. This review focuses on research areas where the coupling between otolith characteristics and fish physiology may yield new insights. Most of the research ideas are by no means new, but rather represent largely forgotten or less-explored research areas. Examples of questions that are fundamental, unanswered and with the potential to yield significant new insights are those related to the coupling of otolith and fish growth through metabolism, and the formation of opaque and translucent growth zones in relation to the physiology of the individual. An integration of visual and chemical data with bioenergetic modelling may yield some of the answers.
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Morrison, Richard N., Glenn A. Cooper, Ben F. Koop, Matthew L. Rise, Andrew R. Bridle, Mark B. Adams, and Barbara F. Nowak. "Transcriptome profiling the gills of amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salarL.): a role for tumor suppressor p53 in AGD pathogenesis?" Physiological Genomics 26, no. 1 (June 2006): 15–34. http://dx.doi.org/10.1152/physiolgenomics.00320.2005.
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Neoparamoeba spp. are amphizoic amoebae with the capacity to colonize the gills of some marine fish, causing AGD. Here, the gill tissue transcriptome response of Atlantic salmon ( Salmo salar L.) to AGD is described. Tanks housing Atlantic salmon were inoculated with Neoparamoeba spp. and fish sampled at time points up to 8 days postinoculation (pi.). Gill tissues were taken from AGD-affected fish, and a DNA microarray was used to compare global gene expression against tissues from AGD-unaffected fish. A total of 206 genes, representing 190 unique transcripts, were reproducibly identified as up- or downregulated in response to Neoparamoeba spp. infection. Informative transcripts having GO biological process identifiers were grouped according to function. Although a number of genes were placed into each category, no distinct patterns were observed. One Atlantic salmon cDNA that was upregulated in infected gill relative to noninfected gill at 114 and 189 h pi. showed significant identity with the Xenopus, mouse, and human anterior gradient-2 (AG-2) homologs. Two Atlantic salmon AG-2 mRNA transcripts, designated asAG-2/1 and asAG-2/2, were cloned, sequenced, and shown to be predominantly expressed in the gill, intestine, and brain of a healthy fish. In AGD-affected fish, differential asAG-2 expression was confirmed in samples used for microarray analyses as well as in AGD-affected gill tissue taken from fish in an independent experiment. The asAG-2 upregulation was restricted to AGD lesions relative to unaffected tissue from the same gill arch, while p53 tumor suppressor protein mRNA was concurrently downregulated in AGD lesions. Differential expression of p53-regulated transcripts, proliferating cell nuclear antigen and growth arrest and DNA damage-inducible gene-45β (GADD45β) in AGD lesions, suggests a role for p53 in AGD pathogenesis. Thus AGD may represent a novel model for comparative analysis of p53 and p53-regulated pathways.
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Rudkowska, Iwona, Bruno Marcotte, Geneviève Pilon, Charles Lavigne, André Marette, and Marie-Claude Vohl. "Fish nutrients decrease expression levels of tumor necrosis factor-α in cultured human macrophages." Physiological Genomics 40, no. 3 (February 2010): 189–94. http://dx.doi.org/10.1152/physiolgenomics.00120.2009.
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Numerous studies have demonstrated the beneficial effects of fish consumption on inflammatory markers. Until now, these beneficial effects of fish consumption have been mostly linked to the omega-3 fatty acids (FA). The objective of the present study was to examine, in vitro, whether expression levels of genes involved in the inflammatory response differ in human macrophages incubated with casein hydrolysates (CH) or fish protein hydrolysates (FPH) in the presence or absence of omega-3 FA compared with omega-3 FA alone. Peripheral blood monocytes differentiated into macrophages from 10 men were incubated in the presence of omega-3 FA (10 μM eicosapentaenoic acid and 5 μM docosahexaenoic acid) or CH or FPH (10, 100, 1,000 μg) with or without omega-3 FA for 48 h. Results demonstrate that expression levels of tumor necrosis factorα ( TNFα) had a tendency to be lower after the addition of FPH alone or CH with omega-3 FA compared with omega-3 FA treatment. Furthermore, the combination of FPH and omega-3 FA synergistically decreased expression levels of TNFα compared to treatment with omega-3 FA or FPH alone. No difference on gene expression levels of interleukin-6 was observed between treatments. In conclusion, these preliminary results suggest that the anti-inflammatory effects of fish consumption can be explained by a synergistic effect of the omega-3 FA with the protein components of fish on TNFα expression and therefore contribute to the beneficial effects of fish consumption. Hence, follow-up studies should be performed to confirm the effects of a diet rich in FPH and omega-3 FA on serum proinflammatory cytokine concentrations.
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Zhao, Yan, Yuan Mei, Hong Ju Chen, Li Tao Zhang, Hui Wang, and Xiang Shan Ji. "Profiling expression changes of genes associated with temperature and sex during high temperature-induced masculinization in the Nile tilapia brain." Physiological Genomics 51, no. 5 (May 1, 2019): 159–68. http://dx.doi.org/10.1152/physiolgenomics.00117.2018.
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Fish sex-determining mechanisms can be classified as genotypic (GSD), temperature (TSD), or genotypic plus temperature effects (GSD+TE). Previous studies have shown that culturing water temperature during thermosensitive periods (TSP) could affect the expression of many genes in the gonad in some fish. However, few studies have focused on gene expression changes in the brain after temperature treatment during TSP in fish species. In this study, three families were developed by crossing XX neomales with XX females and one of them was used for transcriptome analysis. The results showed that a total of 105, 3164 and 4666 DEGs were respectively obtained in FC (female control) vs. FT (high temperature-treated females at TSP), FC vs. MC (male control), and MC vs. FT comparison groups. By profiling analysis, we show that the mRNA expression levels of 16 differentially expressed genes (DEGs) exhibited significant downregulation or upregulation after high temperature treatment and reached a similar level as that in MC. Among the 16 DEGs, LOC100699848 (lysine specific demethylase 6A) and Jarid2 contained JmjC domain, showing the possible important role of JmjC domain in response to temperature treatment in Nile tilapia. Kdm6b (lysine demethylase 6B) and Jarid2 have been shown to play important roles in reptile TSD, showing the relative conservation of underlying regulation mechanisms between TSD in reptile and TSD or GSD+TE in fish species. Finally, the transcriptome profiling was validated by quantitative real-time PCR in nine selected genes. These results provide a direction for investigating the GSD+TE molecular mechanism in fish species.
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Savan, Ram, and Masahiro Sakai. "Genomics of fish cytokines." Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 1, no. 1 (March 2006): 89–101. http://dx.doi.org/10.1016/j.cbd.2005.08.005.
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Lakra, W. S., Vindhya Mohindra, and Kuldeep K. Lal. "Fish genetics and conservation research in India: status and perspectives." Fish Physiology and Biochemistry 33, no. 4 (September 7, 2007): 475–87. http://dx.doi.org/10.1007/s10695-007-9168-z.
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Pelster, Bernd, Adalberto L. Val, and Reinhard Dallinger. "Recent advances in biology and physiology of tropical freshwater fish." Journal of Experimental Zoology Part A: Ecological and Integrative Physiology 335, no. 9-10 (October 18, 2021): 721–22. http://dx.doi.org/10.1002/jez.2552.
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Zhang, Dapeng, Jason T. Popesku, Christopher J. Martyniuk, Huiling Xiong, Paula Duarte-Guterman, Linhui Yao, Xuhua Xia, and Vance L. Trudeau. "Profiling neuroendocrine gene expression changes following fadrozole-induced estrogen decline in the female goldfish." Physiological Genomics 38, no. 3 (August 2009): 351–61. http://dx.doi.org/10.1152/physiolgenomics.00051.2009.
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Teleost fish represent unique models to study the role of neuroestrogens because of the extremely high activity of brain aromatase (AroB; the product of cyp19a1b). Aromatase respectively converts androstenedione and testosterone to estrone and 17β-estradiol (E2). Specific inhibition of aromatase activity by fadrozole has been shown to impair estrogen production and influence neuroendocrine and reproductive functions in fish, amphibians, and rodents. However, very few studies have identified the global transcriptomic response to fadrozole-induced decline of estrogens in a physiological context. In our study, sexually mature prespawning female goldfish were exposed to fadrozole (50 μg/l) in March and April when goldfish have the highest AroB activity and maximal gonadal size. Fadrozole treatment significantly decreased serum E2 levels (4.7 times lower; P = 0.027) and depressed AroB mRNA expression threefold in both the telencephalon ( P = 0.021) and the hypothalamus ( P = 0.006). Microarray expression profiling of the telencephalon identified 98 differentially expressed genes after fadrozole treatment ( q value <0.05). Some of these genes have shown previously to be estrogen responsive in either fish or other species, including rat, mouse, and human. Gene ontology analysis together with functional annotations revealed several regulatory themes for physiological estrogen action in fish brain that include the regulation of calcium signaling pathway and autoregulation of estrogen receptor action. Real-time PCR verified microarray data for decreased (activin-βA) or increased (calmodulin, ornithine decarboxylase 1) mRNA expression. These data have implications for our understanding of estrogen actions in the adult vertebrate brain.
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Tacchi, Luca, James E. Bron, John B. Taggart, Christopher J. Secombes, Ralph Bickerdike, Michael A. Adler, Harald Takle, and Samuel A. M. Martin. "Multiple tissue transcriptomic responses toPiscirickettsia salmonisin Atlantic salmon (Salmo salar)." Physiological Genomics 43, no. 21 (November 2011): 1241–54. http://dx.doi.org/10.1152/physiolgenomics.00086.2011.
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The bacterium Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia (SRS), a severe disease that causes major economic losses to the Atlantic salmon aquaculture industry every year. Little is known about the infective strategy of P. salmonis, which is able to infect, survive within, and replicate inside salmonid macrophages as an intracellular parasite. Similarly there is little knowledge concerning the fish host's response to invasion by this pathogen. We have examined the transcriptional response of postsmolt Atlantic salmon ( Salmo salar) to P. salmonis at 48 h following infection in three tissues, liver, head kidney, and muscle, using an Atlantic salmon oligonucleotide microarray (Salar_2, Agilent 4x44K). The infection led to a large alteration of transcriptional activity in all the tissues studied. In infected salmon 886, 207, and 153 transcripts were differentially expressed in liver, head kidney, and muscle, respectively. Assessment of enrichment for particular biological pathways by gene ontology analysis showed an upregulation of genes involved in oxidative and inflammatory responses in infected fish, indicative of the activation of the innate immune response. The downregulation of genes involved in the adaptive immune response, G protein signaling pathway, and apoptotic process in infected fish may be reflective of mechanisms used by P. salmonis to survive, replicate, and escape host defenses. There was also evidence of differential responses between studied tissues, with protein metabolism being decreased in muscle of infected fish and with a concomitant increase being shown in liver.
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Lewis, Johanne M., Tiago S. Hori, Matthew L. Rise, Patrick J. Walsh, and Suzanne Currie. "Transcriptome responses to heat stress in the nucleated red blood cells of the rainbow trout (Oncorhynchus mykiss)." Physiological Genomics 42, no. 3 (August 2010): 361–73. http://dx.doi.org/10.1152/physiolgenomics.00067.2010.
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The retention of a nucleus in the mature state of fish red blood cells (RBCs) and the ability to easily collect and manipulate blood in nonterminal experiments make blood an ideal tissue on which to study the cellular stress response in fish. Through the use of the cGRASP 16K salmonid microarray, we investigated differences in RBC global gene transcription in fish held under control conditions (11°C) and exposed to heat stress (1 h at 25°C followed by recovery at 11°C). Repeated blood sampling (via a dorsal aorta cannula) enables us to examine the individual stress response over time. Samples were taken preheat stress (representing individual control) and at 4 and 24 h postheat stress (representing early and late transcriptional regulation). Approximately 3,000 microarray features had signal above threshold when hybridized with RBC RNA-derived targets, and cannulation did not have a detectable effect on RBC mRNA expression at the investigated time points. Genes involved in the stress response, immune response, and apoptosis were among those showing the highest dysregulation during both early and late transcriptional regulation. Additionally, genes related to the differentiation and development of blood cells were transcriptionally upregulated at the 24 h time point. This study provides a broader understanding of the mechanisms underpinning the stress response in fish and the discovery of novel genes that are regulated in a stress specific manner. Moreover, salmonid transcripts that are consistently dysregulated in blood in response to heat stress are potential candidates of nonlethal biomarkers of exposure to this particular stressor.
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López-Rodríguez, Ruby, Mario George-Nascimento, and Konrad Górski. "Effects of the cranial parasite Tylodelphys sp. on the behavior and physiology of puye Galaxias maculatus (Jenyns, 1842)." PeerJ 9 (March 22, 2021): e11095. http://dx.doi.org/10.7717/peerj.11095.
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Diplostomatid digeneans are well-known manipulators of the behavior of their intermediate hosts. Unencysted metacercariae of Tylodelphys sp. inhabit the cranial cavity of the fish Galaxias maculatus; however, to date they have not been documented to alter their host behavior. The goal of this study was to evaluate the potential effects of Tylodelphys sp. inhabiting the cranial cavity of Galaxias maculatus on host physiology and swimming behavior as well as its reaction to a simulated predation attempt. Blind experiments in the lab were carried out on 56 fish that were filmed individually. The Fulton condition factor (K) was used as an approximation of nutritional status and a respirometry chamber was used to evaluate oxygen consumption rates of fish. Of the 56 fish, 21 were parasitized by Tylodelphys sp. (mean intensity = 30, range from 1 to 101). Parasitized and non-parasitized fish were similar in condition factor and oxygen consumption rates. Furthermore, the oxygen consumption rate of G. maculatus was not correlated with the abundance of Tylodelphys sp. However, parasitized fish more frequently swam close to the water surface, whereas non-parasitized fish more frequently swam at intermediate depths. When faced with a simulated predator attack, unparasitized fish showed more frequent fleeing behavior as well as a more intense post-fleeing activity. Collectively, these results suggest that Tylodelphys sp. inhabiting the cranial cavity of fish may alter their behavior predisposing them to predation by birds.
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Fernandes, Jorge M. O., Matthew G. Mackenzie, Greg Elgar, Yuzuru Suzuki, Shugo Watabe, James R. Kinghorn, and Ian A. Johnston. "A genomic approach to reveal novel genes associated with myotube formation in the model teleost, Takifugu rubripes." Physiological Genomics 22, no. 3 (August 11, 2005): 327–38. http://dx.doi.org/10.1152/physiolgenomics.00087.2005.
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Little is known about the transcriptional networks that regulate myotube production in vertebrates. In the present study, we have used a genomic approach to discover novel genes associated with myotube formation in fast muscle of the tiger puffer fish, Takifugu rubripes. The number of fast muscle fibers per myotome increased until 1.2 kg body mass, and subsequent growth was by fiber hypertrophy alone. Forward and reverse subtracted cDNA libraries were prepared from a 180-g (myotube +) and a 3.4-kg (myotube −) fish, and 1,452 expressed sequence tags (ESTs) were obtained. After these ESTs were grouped into nonredundant clusters and housekeeping and structural genes were eliminated, 57 genes were selected and quantitative PCR was used to investigate their expression levels in different tissues from independent groups of myotube(−) and myotube(+) fish acclimated to the same environmental conditions and diet. Eleven novel genes were found to be consistently differentially expressed, but only four showed appropriate tissue-specific expression. These four genes were upregulated 5–25 times in fast muscle of myotube(−) relative to myotube(+) growth stages, while their expression remained unchanged in the other tissues studied. The novel genes identified, which are also present in other vertebrate genomes, may play a role in inhibiting myotube formation in vertebrate muscle.
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Salem, Mohamed, P. Brett Kenney, Caird E. Rexroad, and Jianbo Yao. "Microarray gene expression analysis in atrophying rainbow trout muscle: a unique nonmammalian muscle degradation model." Physiological Genomics 28, no. 1 (December 2006): 33–45. http://dx.doi.org/10.1152/physiolgenomics.00114.2006.
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Muscle atrophy is a physiological response to diverse physiological and pathological conditions that trigger muscle deterioration through specific cellular mechanisms. Despite different signals, the biochemical changes in atrophying muscle share many common cascades. Muscle deterioration as a physiological response to the energetic demands of fish vitellogenesis represents a unique model for studying the mechanisms of muscle degradation in non-mammalian animals. A salmonid microarray, containing 16,006 cDNAs, was used to study the transcriptome response to atrophy of fast-switch muscles from gravid rainbow trout compared with sterile fish. Eighty-two unique transcripts were upregulated and 120 transcripts were downregulated in atrophying muscles. Transcripts having gene ontology identifiers were grouped according to their functions. Muscle deterioration was associated with elevated expression of genes involved in the catheptic and collagenase proteolytic pathways; the aerobic production, buffering, and utilization of ATP; and growth arrest; whereas atrophying muscle showed downregulation of genes encoding a serine proteinase inhibitor, enzymes of anaerobic respiration, muscle proteins as well as genes required for RNA and protein biosynthesis/processing. Therefore, gene transcription of the trout muscle atrophy changed in a manner similar to mammalian muscle atrophy. These changes result in an arrest of normal cell growth, protein degradation, and decreased glycolytic cellular respiration that is characteristic of the fast-switch muscle. For the first time, other changes/mechanisms unique to fish were discussed including genes associated with muscle atrophy.
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Wattanadilokchatkun, Pish, Thitipong Panthum, Kitipong Jaisamut, Syed Farhan Ahmad, Sahabhop Dokkaew, Narongrit Muangmai, Prateep Duengkae, Worapong Singchat, and Kornsorn Srikulnath. "Characterization of Microsatellite Distribution in Siamese Fighting Fish Genome to Promote Conservation and Genetic Diversity." Fishes 7, no. 5 (September 22, 2022): 251. http://dx.doi.org/10.3390/fishes7050251.
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The Siamese fighting fish (Betta splendens) is a well-known ornamental fish and emerging model species for studying animal morphology, physiology, and behavior. A key concern of betta inbreeding is the decline in genetic diversity resulting from commercial breeding programs. Therefore, it is essential to develop markers for understanding the genetic bases of the domestication and phenotypic diversification of this species. We utilized the previously assembled genome of Siamese fighting fish to identify and characterize microsatellites and compare their genomic organization across different species. We annotated 812,134 microsatellite loci spanning 30.70 Mb, accounting for 6.57% of the Siamese fighting fish genome. We performed in silico polymorphism screening of microsatellites in the Siamese fighting fish and related species and present these sequences as candidate markers for cross-species amplification. In addition, we successfully validated two microsatellite loci using PCR-based assays in different species, which can promote further genetic characterization of diverse betta lineages. The set of polymorphic markers identified in this study may facilitate the assessment of genetic diversity and population structure and marker-assisted selection, among other applications.
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Jackson, Heather A., Christian R. Marshall, and Eric A. Accili. "Evolution and structural diversification of hyperpolarization-activated cyclic nucleotide-gated channel genes." Physiological Genomics 29, no. 3 (May 2007): 231–45. http://dx.doi.org/10.1152/physiolgenomics.00142.2006.
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Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are members of the voltage-gated channel superfamily and play a critical role in cellular pace-making. Overall sequence conservation is high throughout the family, and channel functions are similar but not identical. Phylogenetic analyses are imperative to understand how these genes have evolved and to make informed comparisons of HCN structure and function. These have been previously limited, however, by the small number of available sequences, from a minimal number of species unevenly distributed over evolutionary time. We have now identified and annotated 31 novel genes from invertebrates, urochordates, fish, amphibians, birds, and mammals. With increased sequence numbers and a broader species representation, a more precise sequence comparison was performed and an evolutionary history for these genes was constructed. Our data confirm the existence of at least four vertebrate paralogs and suggest that these arose via three duplication and diversification events from a single ancestral gene. Additional lineage-specific duplications appear to have occurred in urochordate and fish genomes. Based on exon boundary conservation and phylogenetic analyses, we hypothesize that mammalian gene structure was established, and duplication events occurred, after the divergence of urochordates and before the divergence of fish from the tetrapod lineage. In addition, we identified highly conserved sequence regions that are likely important for general HCN functions, as well as regions with differences conserved among each of the individual paralogs. The latter may underlie more subtle isoform-specific properties that are otherwise masked by the high identity among mammalian orthologs and/or inaccurate alignments between paralogs.
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Mennigen, Jan A., Christopher J. Martyniuk, Kate Crump, Huiling Xiong, E. Zhao, Jason Popesku, Hymie Anisman, Andrew R. Cossins, Xuhua Xia, and Vance L. Trudeau. "Effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus)." Physiological Genomics 35, no. 3 (November 2008): 273–82. http://dx.doi.org/10.1152/physiolgenomics.90263.2008.
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We investigated the effects of fluoxetine, a selective serotonin reuptake inhibitor, on neuroendocrine function and the reproductive axis in female goldfish. Fish were given intraperitoneal injections of fluoxetine twice a week for 14 days, resulting in five injections of 5 μg fluoxetine/g body wt. We measured the monoamine neurotransmitters serotonin, dopamine, and norepinephrine in addition to their metabolites with HPLC. Homovanillic acid, a metabolite in the dopaminergic pathway, increased significantly in the hypothalamus. Plasma estradiol levels were measured by radioimmunoassay and were significantly reduced approximately threefold after fluoxetine treatment. We found that fluoxetine also significantly reduced the expression of estrogen receptor (ER)β1 mRNA by 4-fold in both the hypothalamus and the telencephalon and ERα mRNA by 1.7-fold in the telencephalon. Fluoxetine had no effect on the expression of ERβ2 mRNA in the hypothalamus or telencephalon. Microarray analysis identified isotocin, a neuropeptide that stimulates reproductive behavior in fish, as a candidate gene affected by fluoxetine treatment. Real-time RT-PCR verified that isotocin mRNA was downregulated approximately sixfold in the hypothalamus and fivefold in the telencephalon. Intraperitoneal injection of isotocin (1 μg/g) increased plasma estradiol, providing a potential link between changes in isotocin gene expression and decreased circulating estrogen in fluoxetine-injected fish. Our results reveal targets of serotonergic modulation in the neuroendocrine brain and indicate that fluoxetine has the potential to affect sex hormones and modulate genes involved in reproductive function and behavior in the brain of female goldfish. We discuss these findings in the context of endocrine disruption because fluoxetine has been detected in the environment.
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Feng, Charles Y., Stewart C. Johnson, Tiago S. Hori, Marlies Rise, Jennifer R. Hall, A. Kurt Gamperl, Sophie Hubert, Jennifer Kimball, Sharen Bowman, and Matthew L. Rise. "Identification and analysis of differentially expressed genes in immune tissues of Atlantic cod stimulated with formalin-killed, atypicalAeromonas salmonicida." Physiological Genomics 37, no. 3 (May 2009): 149–63. http://dx.doi.org/10.1152/physiolgenomics.90373.2008.
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Physiological changes, elicited in animal immune tissues by exposure to pathogens, may be studied using functional genomics approaches. We created and characterized reciprocal suppression subtractive hybridization (SSH) cDNA libraries to identify differentially expressed genes in spleen and head kidney tissues of Atlantic cod ( Gadus morhua) challenged with intraperitoneal injections of formalin-killed, atypical Aeromonas salmonicida. Of 4,154 ESTs from four cDNA libraries, 10 genes with immune-relevant functional annotations were selected for QPCR studies using individual fish templates to assess biological variability. Genes confirmed by QPCR as upregulated by A. salmonicida included interleukin-1β, interleukin-8, a small inducible cytokine, interferon regulatory factor 1 (IRF1), ferritin heavy subunit, cathelicidin, and hepcidin. This study is the first large-scale discovery of bacteria-responsive genes in cod and the first to demonstrate upregulation of IRF1 in fish immune tissues as a result of bacterial antigen stimulation. Given the importance of IRF1 in vertebrate immune responses to viral and bacterial pathogens, the full-length cDNA sequence of Atlantic cod IRF1 was obtained and compared with putative orthologous sequences from other organisms. Functional annotations of assembled SSH library ESTs showed that bacterial antigen stimulation caused changes in many biological processes including chemotaxis, regulation of apoptosis, antimicrobial peptide production, and iron homeostasis. Moreover, differences in spleen and head kidney gene expression responses to the bacterial antigens pointed to a potential role for the cod spleen in blood-borne pathogen clearance. Our data show that Atlantic cod immune tissue responses to bacterial antigens are similar to those seen in other fish species and higher vertebrates.
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Metcalfe, J. D., W. J. F. Le Quesne, W. W. L. Cheung, and D. A. Righton. "Conservation physiology for applied management of marine fish: an overview with perspectives on the role and value of telemetry." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1596 (June 19, 2012): 1746–56. http://dx.doi.org/10.1098/rstb.2012.0017.
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Physiological studies focus on the responses of cells, tissues and individuals to stressors, usually in laboratory situations. Conservation and management, on the other hand, focus on populations. The field of conservation physiology addresses the question of how abiotic drivers of physiological responses at the level of the individual alter requirements for successful conservation and management of populations. To achieve this, impacts of physiological effects at the individual level need to be scaled to impacts on population dynamics, which requires consideration of ecology. Successfully realizing the potential of conservation physiology requires interdisciplinary studies incorporating physiology and ecology, and requires that a constructive dialogue develops between these traditionally disparate fields. To encourage this dialogue, we consider the increasingly explicit incorporation of physiology into ecological models applied to marine fish conservation and management. Conservation physiology is further challenged as the physiology of an individual revealed under laboratory conditions is unlikely to reflect realized responses to the complex variable stressors to which it is exposed in the wild. Telemetry technology offers the capability to record an animal's behaviour while simultaneously recording environmental variables to which it is exposed. We consider how the emerging insights from telemetry can strengthen the incorporation of physiology into ecology.
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Mousavi, Seyed Ehsan, G. John Purser, and Jawahar G. Patil. "Embryonic Onset of Sexually Dimorphic Heart Rates in the Viviparous Fish, Gambusia holbrooki." Biomedicines 9, no. 2 (February 8, 2021): 165. http://dx.doi.org/10.3390/biomedicines9020165.
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In fish, little is known about sex-specific differences in physiology and performance of the heart and whether these differences manifest during development. Here for the first time, the sex-specific heart rates during embryogenesis of Gambusia holbrooki, from the onset of the heart rates (HRs) to just prior to parturition, was investigated using light cardiogram. The genetic sex of the embryos was post-verified using a sex-specific genetic marker. Results reveal that heart rates and resting time significantly increase (p < 0.05) with progressive embryonic development. Furthermore, both ventricular and atrial frequencies of female embryos were significantly higher (p < 0.05) than those of their male sibs at the corresponding developmental stages and remained so at all later developmental stages (p < 0.05). In concurrence, the heart rate and ventricular size of the adult females were also significantly (p < 0.05) higher and larger respectively than those of males. Collectively, the results suggest that the cardiac sex-dimorphism manifests as early as late-organogenesis and persists through adulthood in this species. These findings suggest that the cardiac measurements can be employed to non-invasively sex the developing embryos, well in advance of when their phenotypic sex is discernible. In addition, G. holbrooki could serve as a better model to study comparative vertebrate cardiovascular development as well as to investigate anthropogenic and climatic impacts on heart physiology of this species, that may be sex influenced.
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Tomita-Mitchell, Aoy, Donna K. Mahnke, Joshua M. Larson, Sujana Ghanta, Ying Feng, Pippa M. Simpson, Ulrich Broeckel, et al. "Multiplexed quantitative real-time PCR to detect 22q11.2 deletion in patients with congenital heart disease." Physiological Genomics 42A, no. 1 (September 2010): 52–60. http://dx.doi.org/10.1152/physiolgenomics.00073.2010.
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22q11.2 Deletion syndrome (22q11.2 DS) [DiGeorge syndrome type 1 (DGS1)] occurs in ∼1:3,000 live births; 75% of children with DGS1 have severe congenital heart disease requiring early intervention. The gold standard for detection of DGS1 is fluorescence in situ hybridization (FISH) with a probe at the TUPLE1 gene. However, FISH is costly and is typically ordered in conjunction with a karyotype analysis that takes several days. Therefore, FISH is underutilized and the diagnosis of 22q11.2 DS is frequently delayed, often resulting in profound clinical consequences. Our goal was to determine whether multiplexed, quantitative real-time PCR (MQPCR) could be used to detect the haploinsufficiency characteristic of 22q11.2 DS. A retrospective blinded study was performed on 382 subjects who had undergone congenital heart surgery. MQPCR was performed with a probe localized to the TBX1 gene on human chromosome 22, a gene typically deleted in 22q11.2 DS. Cycle threshold (Ct) was used to calculate the relative gene copy number (rGCN). Confirmation analysis was performed with the Affymetrix 6.0 Genome-Wide SNP Array. With MQPCR, 361 subjects were identified as nondeleted with an rGCN near 1.0 and 21 subjects were identified as deleted with an rGCN near 0.5, indicative of a hemizygous deletion. The sensitivity (21/21) and specificity (361/361) of MQPCR to detect 22q11.2 deletions was 100% at an rGCN value drawn at 0.7. One of 21 subjects with a prior clinical (not genetically confirmed) DGS1 diagnosis was found not to carry the deletion, while another subject, not previously identified as DGS1, was detected as deleted and subsequently confirmed via microarray. The MQPCR assay is a rapid, inexpensive, sensitive, and specific assay that can be used to screen for 22q11.2 deletion syndrome. The assay is readily adaptable to high throughput.
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Chapman, Jacqueline M., Lisa A. Kelly, Amy K. Teffer, Kristi M. Miller, and Steven J. Cooke. "Disease ecology of wild fish: opportunities and challenges for linking infection metrics with behaviour, condition, and survival." Canadian Journal of Fisheries and Aquatic Sciences 78, no. 8 (August 2021): 995–1007. http://dx.doi.org/10.1139/cjfas-2020-0315.
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Surmounting evidence supports that infectious agents play a critical role in shaping fish physiology, behaviour, and survival. The exclusion of disease-causing agents from fisheries research has resulted in major knowledge gaps that may limit the predictive capacity of ecological models. A major barrier in wild fisheries epidemiology is the logistical constraints associated with observing disease and obtaining samples from free-ranging fish, restricting the vast majority of research to laboratory studies or aquaculture facilities. For fisheries ecologists, including infectious agents can provide greater insight into observed phenomena, particularly with respect to fish physiology (e.g., metabolism), movement (e.g., migration rates), behaviour (e.g., habitat selection), personality (e.g., bold versus shy), and survival. Here we provide a brief introduction to the current understanding of disease ecology in wild fish and describe technological advances in both epidemiology and fisheries and aquatic sciences that can be used in tandem to create comprehensive studies of disease ecology in wild fishes. Combining nonlethal sampling and molecular genetic-based identification methods with field studies creates vast opportunities for innovative study designs that have the potential to address the true complexity of aquatic ecosystems.
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Chen, Xi, Steve F. Perry, Stéphane Aris-Brosou, Corrado Selva, and Thomas W. Moon. "Characterization and functional divergence of the α1-adrenoceptor gene family: insights from rainbow trout (Oncorhynchus mykiss)." Physiological Genomics 32, no. 1 (December 2007): 142–53. http://dx.doi.org/10.1152/physiolgenomics.00258.2006.
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Presently, three α1-adrenoceptor (AR) types are recognized in vertebrates: α1A-, α1B-, and α1D-ARs. These α1-subtypes have distinct pharmacology and molecular profiles, play crucial roles in metabolic and vascular control, and are the targets for numerous pharmaceuticals, especially those affecting blood pressure and vascular resistance. To better understand the functional divergence within the α1-AR gene family, we sequenced these α1-AR paralogs in the rainbow trout and performed an extensive phylogenetic analysis. We show that these AR genes evolved by duplication events just before the origin of the jawed vertebrates. Our computational analyses suggest that the differences between the three α1-AR subtypes may affect their tissue specificity, ligand specificity, and possibly signal transduction processes and desensitization. We also show that, within each subtype, differences exist between fish and mammalian receptors, both at the transcriptional and at the physiological level. These differences, however, suggest that the role of α1-ARs in fish is more complex than previously thought. Our integrated analysis of the α1-AR gene family suggests that these receptors evolved these distinct features very early within vertebrates.
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Richards, Dylan, Ludivine Renaud, Nisha Agarwal, E. Starr Hazard, John Hyde, and Gary Hardiman. "De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, Sardinops sagax, Scomber japonicus, and Pleuronichthys verticalis." Genes 9, no. 11 (October 25, 2018): 521. http://dx.doi.org/10.3390/genes9110521.
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The monitoring of marine species as sentinels for ecosystem health has long been a valuable tool worldwide, providing insight into how both anthropogenic pollution and naturally occurring phenomena (i.e., harmful algal blooms) may lead to human and animal dietary concerns. The marine environments contain many contaminants of anthropogenic origin that have sufficient similarities to steroid and thyroid hormones, to potentially disrupt normal endocrine physiology in humans, fish, and other animals. An appropriate understanding of the effects of these endocrine disrupting chemicals (EDCs) on forage fish (e.g., sardine, anchovy, mackerel) can lead to significant insight into how these contaminants may affect local ecosystems in addition to their potential impacts on human health. With advancements in molecular tools (e.g., high-throughput sequencing, HTS), a genomics approach offers a robust toolkit to discover putative genetic biomarkers in fish exposed to these chemicals. However, the lack of available sequence information for non-model species has limited the development of these genomic toolkits. Using HTS and de novo assembly technology, the present study aimed to establish, for the first time for Sardinops sagax (Pacific sardine), Scomber japonicas (Pacific chub mackerel) and Pleuronichthys verticalis (hornyhead turbot), a de novo global transcriptome database of the liver, the primary organ involved in detoxification. The assembled transcriptomes provide a foundation for further downstream validation, comparative genomic analysis and biomarker development for future applications in ecotoxicogenomic studies, as well as environmental evaluation (e.g., climate change) and public health safety (e.g., dietary screening).
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Jastroch, Martin, Sven Wuertz, Werner Kloas, and Martin Klingenspor. "Uncoupling protein 1 in fish uncovers an ancient evolutionary history of mammalian nonshivering thermogenesis." Physiological Genomics 22, no. 2 (July 14, 2005): 150–56. http://dx.doi.org/10.1152/physiolgenomics.00070.2005.
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Uncoupling proteins (UCPs) increase proton leakage across the inner mitochondrial membrane. Thereby, UCP1 in brown adipose tissue dissipates proton motive force as heat. This mechanism of nonshivering thermogenesis is considered as a monophyletic trait of endothermic placental mammals that emerged about 140 million years ago and provided a crucial advantage for life in the cold. The paralogues UCP2 and UCP3 are probably not thermogenic proteins but convey mild uncoupling, which may serve to reduce the rate of mitochondrial reactive oxygen species production. Both are present in endotherms (mammals and birds), but so far only UCP2 has been identified in ectothermic vertebrates (fish and amphibia). The evolution of UCPs is of general interest in the search for the origin of mammalian UCP1-mediated nonshivering thermogenesis. We here show the presence of UCP1 and UCP3 in ectothermic teleost fish species using comparative genomics, phylogenetic inference, and gene expression analysis. In the common carp ( Cyprinus carpio), UCP1 is predominantly expressed in the liver and strongly diminished in response to cold exposure, thus contrasting the cold-induced expression of mammalian UCP1 in brown adipose tissue. UCP3 mRNA is only found in carp skeletal muscle with expression levels increased fivefold in response to fasting. Our findings disprove the monophyletic nature of UCP1 in placental mammals and demonstrate that all three members of the core UCP family were already present before the divergence of ray-finned and lobe-finned vertebrate lineages about 420 million years ago.
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Gallego, V., and J. F. Asturiano. "Sperm motility in fish: technical applications and perspectives through CASA-Mot systems." Reproduction, Fertility and Development 30, no. 6 (2018): 820. http://dx.doi.org/10.1071/rd17460.
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Although a relatively high number of sperm quality biomarkers have been reported over the years in several fish species, sperm motility is nowadays considered the best biomarker for fish spermatozoa. The first scientific reports focusing on fish sperm motility date from a century ago, but the objective assessment allowed by computer-aided sperm analysis (CASA-Mot) systems was not applied to fish species until the mid-1980s. Since then, a high number of sperm kinetic parameters from more than 170 fish species have been reported in more than 700 scientific articles, covering a wide range of topics, such as sperm physiology, sperm storage, broodstock management, the phenomenon of sperm competition, ecotoxicology and understanding the life cycle of the species. The sperm kinetic parameters provided by CASA-Mot systems can serve as powerful and useful tools for aquaculture and ecological purposes, and this review provides an overview of the major research areas in which fish sperm motility assessment by a CASA-Mot system has been used successfully.
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Brown, A. R., L. Gunnarsson, E. Kristiansson, and C. R. Tyler. "Assessing variation in the potential susceptibility of fish to pharmaceuticals, considering evolutionary differences in their physiology and ecology." Philosophical Transactions of the Royal Society B: Biological Sciences 369, no. 1656 (November 19, 2014): 20130576. http://dx.doi.org/10.1098/rstb.2013.0576.
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Fish represent the planet's most diverse group of vertebrates and they can be exposed to a wide range of pharmaceuticals. For practical reasons, extrapolation of pharmaceutical effects from ‘model’ species to other fish species is adopted in risk assessment. Here, we critically assess this approach. First, we show that between 65% and 86% of human drug targets are evolutionarily conserved in 12 diverse fish species. Focusing on nuclear steroid hormone receptors, we further show that the sequence of the ligand binding domain that plays a key role in drug potency is highly conserved, but there is variation between species. This variation for the oestrogen receptor, however, does not obviously account for observed differences in receptor activation. Taking the synthetic oestrogen ethinyloestradiol as a test case, and using life-table-response experiments, we demonstrate significant reductions in population growth in fathead minnow and medaka, but not zebrafish, for environmentally relevant exposures. This finding contrasts with zebrafish being ranked as more ecologically susceptible, according to two independent life-history analyses. We conclude that while most drug targets are conserved in fish, evolutionary divergence in drug-target activation, physiology, behaviour and ecological life history make it difficult to predict population-level effects. This justifies the conventional use of at least a 10× assessment factor in pharmaceutical risk assessment, to account for differences in species susceptibility.
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Martin, S. A. M., J. B. Taggart, P. Seear, J. E. Bron, R. Talbot, A. J. Teale, G. E. Sweeney, et al. "Interferon type I and type II responses in an Atlantic salmon (Salmo salar) SHK-1 cell line by the salmon TRAITS/SGP microarray." Physiological Genomics 32, no. 1 (December 2007): 33–44. http://dx.doi.org/10.1152/physiolgenomics.00064.2007.
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Interferons (IFNs) are cytokines that have proinflammatory, antiviral, and immunomodulatory effects and play a central role during a host response to pathogens. The IFN family contains both type I and type II molecules. While there are a number of type I IFNs, there is only one type II IFN. Recently both type I and type II IFN genes have been cloned in salmonid fish and recombinant proteins produced showing IFN activity. We have stimulated an Atlantic salmon cell line (SHK-1) with both type I and type II recombinant salmonid IFNs and analyzed the transcriptional response by microarray analysis. Cells were exposed to recombinant IFNs for 6 or 24 h or left unexposed as controls. RNA was hybridized to an Atlantic salmon cDNA microarray (salmon 17K feature TRAITS/SGP array) in order to assess differential gene expression in response to IFN exposure. For IFN I and II, 47 and 72 genes were stimulated, respectively; most genes were stimulated by a single IFN type, but some were affected by both IFNs, indicating coregulation of the IFN response in fish. Real-time PCR analysis was employed to confirm the microarray results for selected differentially expressed genes in both a cell line and primary leukocyte cultures.
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Kostyniuk, Daniel J., Lucie Marandel, Mais Jubouri, Karine Dias, Robson F. de Souza, Dapeng Zhang, Christopher J. Martyniuk, Stéphane Panserat, and Jan A. Mennigen. "Profiling the rainbow trout hepatic miRNAome under diet-induced hyperglycemia." Physiological Genomics 51, no. 9 (September 1, 2019): 411–31. http://dx.doi.org/10.1152/physiolgenomics.00032.2019.
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Carnivorous rainbow trout exhibit prolonged postprandial hyperglycemia when fed a diet exceeding 20% carbohydrate content. This poor capacity to utilize carbohydrates has led to rainbow trout being classified as “glucose-intolerant” (GI). The metabolic phenotype has spurred research to identify the underlying cellular and molecular mechanisms of glucose intolerance, largely because carbohydrate-rich diets provide economic and ecological advantages over traditionally used fish meal, considered unsustainable for rainbow trout aquaculture operations. Evidence points to a contribution of hepatic intermediary carbohydrate and lipid metabolism, as well as upstream insulin signaling. Recently, microRNAs (miRNAs), small noncoding RNAs acting as negative posttranscriptional regulators affecting target mRNA stability and translation, have emerged as critical regulators of hepatic control of glucose-homeostasis in mammals, revealing that dysregulated hepatic miRNAs might play a role in organismal hyperglycemia in metabolic disease. To determine whether hepatic regulatory miRNA networks may contribute to GI in rainbow trout, we induced prolonged postprandial hyperglycemia in rainbow trout by using a carbohydrate-rich diet and profiled genome-wide hepatic miRNAs in hyperglycemic rainbow trout compared with fasted trout and trout fed a diet devoid of carbohydrates. Using small RNA next-generation sequencing and real-time RT-PCR validation, we identified differentially regulated hepatic miRNAs between these groups and used an in silico approach to predict bona fide mRNA targets and enriched pathways. Diet-induced hyperglycemia resulted in differential regulation of hepatic miRNAs compared with fasted fish. Some of the identified miRNAs, such as miRNA-27b-3p and miRNA-200a-3p, are known to be responsive to hyperglycemia in the liver of hyperglycemic glucose-tolerant fish and mammals, suggesting an evolutionary conserved regulation. Using Gene Ontology term-based enrichment analysis, we identify intermediate carbohydrate and lipid metabolism and insulin signaling as potential targets of posttranscriptional regulation by hyperglycemia-regulated miRNAs and provide correlative expression analysis of specific predicted miRNA-target pairs. This study identifies hepatic miRNAs in rainbow trout that exhibit differential postprandial expression in response to diets with different carbohydrate content and predicts posttranscriptionally regulated target mRNAs enriched for pathways involved in glucoregulation. Together, these results provide a framework for testable hypotheses of functional involvement of specific hepatic miRNAs in GI in rainbow trout.
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Fitzpatrick, J. L., J. K. Desjardins, N. Milligan, K. A. Stiver, R. Montgomerie, and S. Balshine. "Female-mediated causes and consequences of status change in a social fish." Proceedings of the Royal Society B: Biological Sciences 275, no. 1637 (January 29, 2008): 929–36. http://dx.doi.org/10.1098/rspb.2007.1449.
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In highly social species, dominant individuals often monopolize reproduction, resulting in reproductive investment that is status dependent. Yet, for subordinates, who typically invest less in reproduction, social status can change and opportunities to ascend to dominant social positions are presented suddenly, requiring abrupt changes in behaviour and physiology. In this study, we examined male reproductive anatomy, physiology and behaviour following experimental manipulations of social status in the cooperatively breeding cichlid fish, Neolamprologus pulcher . This unusual fish species lives in permanent social groups composed of a dominant breeding pair and 1–20 subordinates that form a linear social dominance hierarchy. By removing male breeders, we created 18 breeding vacancies and thus provided an opportunity for subordinate males to ascend in status. Dominant females play an important role in regulating status change, as males successfully ascended to breeder status only when they were slightly larger than the female breeder in their social group. Ascending males rapidly assumed behavioural dominance, demonstrated elevated gonadal investment and androgen concentrations compared with males remaining socially subordinate. Interestingly, to increase gonadal investment ascending males appeared to temporarily restrain somatic growth. These results highlight the complex interactions between social status, reproductive physiology and group dynamics, and underscore a convergent pattern of reproductive investment among highly social, cooperative species.
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Adamovsky, Ondrej, Joseph H. Bisesi, and Christopher J. Martyniuk. "Plastics in our water: Fish microbiomes at risk?" Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 39 (September 2021): 100834. http://dx.doi.org/10.1016/j.cbd.2021.100834.
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Twardek, W. M., A. Ekström, E. J. Eliason, R. J. Lennox, E. Tuononen, A. E. I. Abrams, A. L. Jeanson, and S. J. Cooke. "Field assessments of heart rate dynamics during spawning migration of wild and hatchery-reared Chinook salmon." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1830 (June 14, 2021): 20200214. http://dx.doi.org/10.1098/rstb.2020.0214.
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During spawning, adult Pacific salmonids ( Oncorhynchus spp . ) complete challenging upriver migrations during which energy and oxygen delivery must be partitioned into activities such as locomotion, maturation and spawning behaviours under the constraints of an individual's cardiac capacity. To advance our understanding of cardiac function in free-swimming fishes, we implanted migrating adult Chinook salmon ( Oncorhynchus tshawytscha ) collected near the mouth of the Sydenham River, Ontario, with heart rate ( f H ) biologgers that recorded f H every 3 min until these semelparous fish expired on spawning grounds several days later. Fundamental aspects of cardiac function were quantified, including resting, routine and maximum f H , as well as scope for f H (maximum−resting f H ). Predictors of f H were explored using generalized least-squares regression, including water temperature, discharge, fish size and fish origin (wild versus hatchery). Heart rate was positively correlated with water temperature, which aligned closely with daily and seasonal shifts. Wild fish had slower resting heart rates than hatchery fish, which led to significantly higher scope for f H . Our findings suggest that wild salmon may have better cardiac capacity during migration than hatchery fish, potentially promoting migration success in wild fish. This article is part of the theme issue ‘Measuring physiology in free-living animals (Part I)’.
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Liu, Shikai, Xiuli Wang, Fanyue Sun, Jiaren Zhang, Jianbin Feng, Hong Liu, K. V. Rajendran, et al. "RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish." Physiological Genomics 45, no. 12 (June 15, 2013): 462–76. http://dx.doi.org/10.1152/physiolgenomics.00026.2013.
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Temperature is one of the most prominent abiotic factors affecting ectotherms. Most fish species, as ectotherms, have extraordinary ability to deal with a wide range of temperature changes. While the molecular mechanism underlying temperature adaptation has long been of interest, it is still largely unexplored with fish. Understanding of the fundamental mechanisms conferring tolerance to temperature fluctuations is a topic of increasing interest as temperature may continue to rise as a result of global climate change. Catfish have a wide natural habitat and possess great plasticity in dealing with environmental variations in temperature. However, no studies have been conducted at the transcriptomic level to determine heat stress-induced gene expression. In the present study, we conducted an RNA-Seq analysis to identify heat stress-induced genes in catfish at the transcriptome level. Expression analysis identified a total of 2,260 differentially expressed genes with a cutoff of twofold change. qRT-PCR validation suggested the high reliability of the RNA-Seq results. Gene ontology, enrichment, and pathway analyses were conducted to gain insight into physiological and gene pathways. Specifically, genes involved in oxygen transport, protein folding and degradation, and metabolic process were highly induced, while general protein synthesis was dramatically repressed in response to the lethal temperature stress. This is the first RNA-Seq-based expression study in catfish in response to heat stress. The candidate genes identified should be valuable for further targeted studies on heat tolerance, thereby assisting the development of heat-tolerant catfish lines for aquaculture.
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Roy, Soumita, Sanraja Muchahary, Heikham Dayami, Bichitra Narzary, and Bronson Kumar Khangembam. "Studies on the feeding habit and digestive enzyme activities in three small indigenous fish species from Assam, India." Journal of Experimental Biology and Agricultural Sciences 10, no. 4 (August 30, 2022): 902–11. http://dx.doi.org/10.18006/2022.10(4).902.911.
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Knowledge of the feeding habit and the digestive physiology of a fish is important in making appropriate strategies for feed development and successful culture. Nutrient-rich small indigenous fish species (SIFs) are abundant in Assam, India. Puntius sophore, Mystus tengara, and Trichogaster fasciata of Gossaigaon, Assam are important SIFs for the local rural population, and also potential candidates for ornamental fish culture. The present study aims to evaluate the feeding habit and digestive enzyme activities of these species. Data obtained from the relative gut length and gut content analysis suggested that M. tengara is a carnivorous fish and the rest two fishes are omnivorous in habit. Further, the relative gut length was highest in T. fasciata (4.20±0.45) and lowest in M. tengara (0.55±0.11). Digestive enzyme activity indicates a correlation with the dietary habit of the fish. Further, total protease, trypsin, and amylase activity was reported highest in P. sophore. Acid protease pepsin was found to be significantly higher in M. tengara complementing its carnivorous habit and gut anatomy. The present study has established some important information on the digestive enzyme characteristics and feeding habits of the three fish species. This information might be useful in the development of suitable feed for the fish species for their culture.
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Vatsos, I. N. "Standardizing the microbiota of fish used in research." Laboratory Animals 51, no. 4 (December 8, 2016): 353–64. http://dx.doi.org/10.1177/0023677216678825.
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Little attention has been paid to the effects of fish microbiotas on the reproducibility and comparability of fish studies so far. Extrinsic and intrinsic factors, such as water quality, environmental microbial populations, diet, host genetic profile, gender, age and stress status, affect fish microbiotas and create significant inter- and intra-species variations. Fish microbiotas play critical roles in many key aspects of host physiology, such as protection against pathogens, digestion and development of the digestive tract and the local immune system. Thus, greater effort should be invested in standardizing the microbiological profiles of research fish. In this context, issues requiring consideration include the establishment of isogenic and isobiotic fish lines, the standardization of rearing conditions and the development of appropriate tests to adequately describe microbial populations. There are many challenges involved in each of these issues, and the research community must decide which aspects should be standardized for each species and each type of research. For all studies in which microbiota is expected to exert an influence, thorough reporting is of paramount importance. Every step towards standardization increases study quality and simultaneously contributes to reducing the number of fish used in research, which is a legal and ethical obligation.
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Brønstad, Aurora. "Good Anesthesia Practice for Fish and Other Aquatics." Biology 11, no. 9 (September 15, 2022): 1355. http://dx.doi.org/10.3390/biology11091355.
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Fish and other aquatic animals represent a significant number of species with diverse physiology, size, and housing condition needs. Anesthesia may be necessary for several husbandry procedures as well as treatment of diseases, surgery, or experimental procedures. Choice of drugs and detailed procedures for anesthesia must be adapted to the species in question—there is no “one size fits all” solution. However, there are some basic principles that apply for good anesthetic practice of all animals. These principles include the preparations of animals, personnel, facilities and equipment, monitoring animals under anesthesia, as well as post-anesthetic care to be sure that animals are not lost in the recovery phase. Good anesthesia practice also includes the competence and commitment of personnel involved. Based on professional judgement, key factors will be the focus of this text.
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Kalujnaia, Svetlana, Iain S. McWilliam, Vitalii A. Zaguinaiko, Anja L. Feilen, John Nicholson, Neil Hazon, Christopher P. Cutler, and Gordon Cramb. "Transcriptomic approach to the study of osmoregulation in the European eelAnguilla anguilla." Physiological Genomics 31, no. 3 (November 2007): 385–401. http://dx.doi.org/10.1152/physiolgenomics.00059.2007.
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In euryhaline teleosts, osmoregulation is a fundamental and dynamic process that is essential for the maintenance of ion and water balance, especially when fish migrate between fresh water (FW) and sea water (SW) environments. The European eel has proved to be an excellent model species to study the molecular and physiological adaptations associated with this osmoregulatory plasticity. The life cycle of the European eel includes two migratory periods, the second being the migration of FW eels back to the Sargasso Sea for reproduction. Various anatomical and physiological changes allow the successful transition to SW. The aim of this study was to use a microarray approach to screen the osmoregulatory tissues of the eel for changes in gene expression following acclimation to SW. Tissues were sampled from fish at selected intervals over a 5-mo period following FW/SW transfer, and RNA was isolated. Suppressive subtractive hybridization was used for enrichment of differentially expressed genes. Microarrays comprising 6,144 cDNAs from brain, gill, intestine, and kidney libraries were hybridized with appropriate targets and analyzed; 229 differentially expressed clones with unique sequences were identified. These clones represented the sequences for 95 known genes, with the remaining sequences (59%) being unknown. The results of the microarray analysis were validated by quantification of 28 differentially expressed genes by Northern blotting. A number of the differentially expressed genes were already known to be involved in osmoregulation, but the functional roles of many others, not normally associated with ion or water transport, remain to be characterized.
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Genge, Christine E., William S. Davidson, and Glen F. Tibbits. "Adult teleost heart expresses two distinct troponin C paralogs: cardiac TnC and a novel and teleost-specific ssTnC in a chamber- and temperature-dependent manner." Physiological Genomics 45, no. 18 (September 15, 2013): 866–75. http://dx.doi.org/10.1152/physiolgenomics.00074.2013.
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The teleost-specific whole genome duplication created multiple copies of genes allowing for subfunctionalization of isoforms. In this study, we show that the teleost cardiac Ca2+-binding troponin C (TnC) is the product of two distinct genes: cardiac TnC (cTnC, TnnC1a) and a fish-specific slow skeletal TnC (ssTnC, TnnC1b). The ssTnC gene is novel to teleosts as mammals have a single gene commonly referred as cTnC but which is also expressed in slow skeletal muscle. In teleosts, the data strongly indicate that these are two TnC genes are different paralogs. Because we determined that ssTnC exists across many teleosts but not in basal ray-finned fish (e.g., bichir), we propose that these paralogs are the result of an ancestral tandem gene duplication persisting only in teleosts. Quantification of mRNA levels was used to demonstrate distinct expression localization patterns of the paralogs within the chambers of the heart. In the adult zebrafish acclimated at 28°C, ssTnC mRNA levels are twofold greater than cTnC mRNA levels in the atrium, whereas cTnC mRNA was almost exclusively expressed in the ventricle. Meanwhile, rainbow trout acclimated at 5°C showed cTnC mRNA levels in both chambers significantly greater than ssTnC. Distinct responses to temperature acclimation were also quantified in both adult zebrafish and rainbow trout, with mRNA in both chambers shifting to express higher levels of cTnC in 18°C acclimated zebrafish and 5°C acclimated trout. Possible subfunctionalization of TnC isoforms may provide insight into how teleosts achieve physiological versatility in chamber-specific contractile properties.
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Santos, E. M., V. L. Workman, G. C. Paull, A. L. Filby, K. J. W. Van Look, P. Kille, and C. R. Tyler. "Molecular basis of sex and reproductive status in breeding zebrafish." Physiological Genomics 30, no. 2 (July 2007): 111–22. http://dx.doi.org/10.1152/physiolgenomics.00284.2006.
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The zebrafish ( Danio rerio) is used extensively as a model species for studies on vertebrate development and for assessing chemical effects on reproduction. Despite this, the molecular mechanisms controlling zebrafish reproduction are poorly understood. We analyzed the transcriptomic profiles of the gonads of individual zebrafish, using a 17k oligonucleotide microarray, to define the molecular basis of sex and reproductive status in sexually mature fish. The gonadal transcriptome differed substantially between sexes. Among the genes overexpressed in females, 11 biological processes were overrepresented including mitochondrion organization and biogenesis, and cell growth and/or maintenance. Among the genes overexpressed in males, six biological processes were overrepresented including protein biosynthesis and protein metabolism. Analysis of the expression of gene families known to be involved in reproduction identified a number of genes differentially expressed between ovaries and testes including a number of sox genes and genes belonging to the insulin-like growth factor and the activin-inhibin pathways. Real-time quantitative PCR confirmed the expression profiles for nine of the most differentially expressed genes and indicated that many transcripts are likely to be switched off in one of the sexes in the gonads of adult fish. Significant differences were seen between the gonad transcriptomes of individual reproductively active females reflecting their stage of maturation, whereas the testis transcriptomes were remarkably similar between individuals. In summary, we have identified molecular processes associated with (gonadal) sex specificity in breeding zebrafish and established a strong relationship between individual ovarian transcriptomes and reproductive status in females.
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Saito, Shigeru, and Ryuzo Shingai. "Evolution of thermoTRP ion channel homologs in vertebrates." Physiological Genomics 27, no. 3 (December 2006): 219–30. http://dx.doi.org/10.1152/physiolgenomics.00322.2005.
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In mammalian thermosensation, nine temperature-sensitive ion channels that are activated by distinct temperature thresholds have been identified as thermosensors. These ion channels belong to the transient receptor potential (TRP) superfamily and are referred to as “thermoTRPs” (TRPV1, TRPV2, TRPV3, TRPV4, TRPM2, TRPM4, TRPM5, TRPM8, and TRPA1). To elucidate the evolutionary processes of thermoTRPs, we conducted comprehensive searches for mammalian thermoTRP gene homologs in the draft genome sequences of chicken ( Gallus gallus), western clawed frog ( Xenopus tropicalis), zebrafish ( Danio rerio), and pufferfish ( Fugu rubripes). Newly identified homologs were compared with known thermoTRPs, and phylogenetic analyses were conducted. Our comparative analyses revealed that most of the mammalian thermo-TRP members already existed in the common ancestor of fishes and tetrapods. Tetrapods shared almost the same repertoire, except that the western clawed frog expanded TRPV4s (six copies) and TRPM8s (two copies), which were diversified considerably. Comparisons of nonsynonymous and synonymous substitution rates among TRPV4s suggested that one copy of the TRPV4 channel in the western clawed frog retained its original function, while the other copies diversified and obtained slightly different properties. In fish lineages, several members of thermo-TRPs have duplicated in the whole genome duplication occurred in the ancestral ray-finned fish; however, some of the copies have subsequently been lost. Furthermore, fishes do not possess the three members of thermoTRPs existed in mammals, e.g., thermoTRPs activated by noxious heat, warm, and cool temperatures. Our results suggest that thermosensation mechanisms have changed through vertebrate evolution with respect to thermosensor repertoires.
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Yoder, Jeffrey A. "Investigating the morphology, function and genetics of cytotoxic cells in bony fish." Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 138, no. 3 (July 2004): 271–80. http://dx.doi.org/10.1016/j.cca.2004.03.008.
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Dysin, Artem P., Yuri S. Shcherbakov, Olga A. Nikolaeva, Valerii P. Terletskii, Valentina I. Tyshchenko, and Natalia V. Dementieva. "Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics." Genes 13, no. 12 (November 27, 2022): 2221. http://dx.doi.org/10.3390/genes13122221.
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The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Heras, Joseph, Mahul Chakraborty, J. J. Emerson, and Donovan P. German. "Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish." Proceedings of the Royal Society B: Biological Sciences 287, no. 1921 (February 19, 2020): 20192327. http://dx.doi.org/10.1098/rspb.2019.2327.
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Adopting a new diet is a significant evolutionary change, and can profoundly affect an animal's physiology, biochemistry, ecology and genome. To study this evolutionary transition, we investigated the physiology and genomics of digestion of a derived herbivorous fish, Cebidichthys violaceus . We sequenced and assembled its genome (N50 = 6.7 Mb) and digestive transcriptome, and revealed the molecular changes related to digestive enzymes (carbohydrases, proteases and lipases), finding abundant evidence of molecular adaptation. Specifically, two gene families experienced expansion in copy number and adaptive amino acid substitutions: amylase and carboxyl ester lipase ( cel ), which are involved in the digestion of carbohydrates and lipids, respectively. Both show elevated levels of gene expression and increased enzyme activity. Because carbohydrates are abundant in the prickleback's diet and lipids are rare, these findings suggest that such dietary specialization involves both exploiting abundant resources and scavenging rare ones, especially essential nutrients, like essential fatty acids.
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Ikeda, Daisuke, Yosuke Ono, Phil Snell, Yvonne J. K. Edwards, Greg Elgar, and Shugo Watabe. "Divergent evolution of the myosin heavy chain gene family in fish and tetrapods: evidence from comparative genomic analysis." Physiological Genomics 32, no. 1 (December 2007): 1–15. http://dx.doi.org/10.1152/physiolgenomics.00278.2006.
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Myosin heavy chain genes ( MYHs) are the most important functional domains of myosins, which are highly conserved throughout evolution. The human genome contains 15 MYHs, whereas the corresponding number in teleost appears to be much higher. Although teleosts comprise more than one-half of all vertebrate species, our knowledge of MYHs in teleosts is rather limited. A comprehensive analysis of the torafugu ( Takifugu rubripes) genome database enabled us to detect at least 28 MYHs, almost twice as many as in humans. RT-PCR revealed that at least 16 torafugu MYH representatives (5 fast skeletal, 3 cardiac, 2 slow skeletal, 1 superfast, 2 smooth, and 3 nonmuscle types) are actually transcribed. Among these, MYH M743-2 and MYH M5 of fast and slow skeletal types, respectively, are expressed during development of torafugu embryos. Syntenic analysis reveals that torafugu fast skeletal MYHs are distributed across five genomic regions, three of which form clusters. Interestingly, while human fast skeletal MYHs form one cluster, its syntenic region in torafugu is duplicated, although each locus contains just a single MYH in torafugu. The results of the syntenic analysis were further confirmed by corresponding analysis of MYHs based on databases from Tetraodon, zebrafish, and medaka genomes. Phylogenetic analysis suggests that fast skeletal MYHs evolved independently in teleosts and tetrapods after fast skeletal MYHs had diverged from four ancestral MYHs.
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Gallo, Benjamin D., John M. Farrell, and Brian Leydet. "Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species." PeerJ 8 (December 18, 2020): e10237. http://dx.doi.org/10.7717/peerj.10237.
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Research on the gut microbiome of host organisms has rapidly advanced with next generation sequencing (NGS) and high-performance computing capabilities. Nonetheless, gut microbiome research has focused on mammalian organisms in laboratory settings, and investigations pertaining to wild fish gut microbiota remain in their infancy. We applied a procedure (available at https://github.com/bngallo1994) for sampling of the fish gut for use in NGS to describe microbial community structure. Our approach allowed for high bacterial OTU diversity coverage (>99.7%, Good’s Coverage) that led to detection of differences in gut microbiota of an invasive (Round Goby) and native (Yellow Bullhead) fish species and collected from the upper St. Lawrence River, an environment where the gut microbiota of fish had not previously been tested. Additionally, results revealed habitat level differences in gut microbiota using two distance metrics (Unifrac, Bray–Curtis) between nearshore littoral and offshore profundal collections of Round Goby. Species and habitat level differences in intestinal microbiota may be of importance in understanding individual and species variation and its importance in regulating fish health and physiology.
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Chopelet, J., S. Mariani, and R. Waples. "Does sex-change increase population genetic structure in marine fish?" Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 150, no. 3 (July 2008): S203. http://dx.doi.org/10.1016/j.cbpa.2008.04.568.
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Torres-Paz, Jorge, Carole Hyacinthe, Constance Pierre, and Sylvie Rétaux. "Towards an integrated approach to understand Mexican cavefish evolution." Biology Letters 14, no. 8 (August 2018): 20180101. http://dx.doi.org/10.1098/rsbl.2018.0101.
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The Mexican tetra, Astyanax mexicanus , comes in two forms: a classical river-dwelling fish and a blind and depigmented cave-dwelling fish. The two morphotypes are used as models for evolutionary biology, to decipher mechanisms of morphological and behavioural evolution in response to environmental change. Over the past 40 years, insights have been obtained from genetics, developmental biology, physiology and metabolism, neuroscience, genomics, population biology and ecology. Here, we promote the idea that A. mexicanus , as a model, has reached a stage where an integrated approach or a multi-disciplinary method of analysis, whereby a phenomenon is examined from several angles, is a powerful tool that can be applied to understand general evolutionary processes. Mexican cavefish have undergone considerable selective pressure and extreme morphological evolution, an obvious advantage to contribute to our understanding of evolution through comparative analyses and to pinpoint the specific traits that may have helped their ancestors to colonize caves.
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Purcell, Maureen K., Kelly D. Smith, Alan Aderem, Leroy Hood, James R. Winton, and Jared C. Roach. "Conservation of Toll-like receptor signaling pathways in teleost fish." Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 1, no. 1 (March 2006): 77–88. http://dx.doi.org/10.1016/j.cbd.2005.07.003.
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Purdom, C. E. "Genetic techniques for control of sexuality in fish farming." Fish Physiology and Biochemistry 2, no. 1-4 (October 1986): 3–8. http://dx.doi.org/10.1007/bf02264069.
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