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Exploring early micronutrient deficiencies in rainbow Trout (Oncorhynchus mykiss) by next-generation sequencing technology--from black box to functional genomics.

Olsvik PA, Hemre GI, Waagbø R - PLoS ONE (2013)

Bottom Line: This work studies final nutritional status and transcriptional responses of rainbow trout (Oncorhynchus mykiss Walbaum 1792) (28 g) after a 10 week feeding experiment designed to elucidate the effect of adding a vitamin and mineral premix on growth, health, and nutritional endpoints.Processes related to lipid metabolism, peptide hydrolysis, oxygen transportation, and growth development were mostly affected.Considering the transcriptomics data relative to changes in nutritional status from the feeding study and the background phenotypic outcome of growth performance and gill histopathology, the outcome of the transcriptional profiling are suggested to be mainly related to suboptimal pantothenic acid and vitamin C nutrition.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Nutrition and Seafood Research (NIFES), Bergen, Norway. pal.olsvik@nifes.no

ABSTRACT
This work studies final nutritional status and transcriptional responses of rainbow trout (Oncorhynchus mykiss Walbaum 1792) (28 g) after a 10 week feeding experiment designed to elucidate the effect of adding a vitamin and mineral premix on growth, health, and nutritional endpoints. Juvenile fish were fed a either a diet supplemented with a vitamin and mineral premix (Diet S) or the same diet without premix supplementation (Diet U). The analyzed micronutrient composition of diets differed accordingly. Pooled livers from 15 fish from each dietary group were used to create suppression subtractive hybridization (SSH) cDNA libraries that were sequenced with 454 FLX GS Titanium Technology. In total 552 812 reads were sequenced from the two cDNA libraries. Ingenuity pathway analysis (IPA) was then used to characterize the hepatic transcriptome of the two dietary groups of rainbow trout. In the present communication we discuss how selected micronutrients may affect the transcriptome at suboptimal status by directly impacting the cellular metabolism, functions, and structures, and by introducing respective compensatory mechanisms. Processes related to lipid metabolism, peptide hydrolysis, oxygen transportation, and growth development were mostly affected. Considering the transcriptomics data relative to changes in nutritional status from the feeding study and the background phenotypic outcome of growth performance and gill histopathology, the outcome of the transcriptional profiling are suggested to be mainly related to suboptimal pantothenic acid and vitamin C nutrition.

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Related in: MedlinePlus

Significantly different expression of A) cyp1a3, and B) hmox1 in liver of rainbow trout fed diets with unsupplemented (Diet U) or supplemented (Diet S) levels of a vitamin and mineral premix.(Mean ± SEM). * P<0.05.
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pone-0069461-g004: Significantly different expression of A) cyp1a3, and B) hmox1 in liver of rainbow trout fed diets with unsupplemented (Diet U) or supplemented (Diet S) levels of a vitamin and mineral premix.(Mean ± SEM). * P<0.05.

Mentions: Based on the findings from the SSH cDNA libraries, the transcriptional levels of a set of genes were determined with RT-qPCR from a total of 30 individual rainbow trout (15 fish from each dietary group). These genes were selected as potential markers of pathways suggested affected by the SSH cDNA libraries or as expected candidate biomarkers based on current knowledge. Table 3 lists the target genes selected for RT-qPCR verification. Only two out of 17 evaluated transcripts were significantly different between the two dietary groups (t-test). These were cyp1a3 (Figure 4A), and hmox1 (Figure 4B). We do at present not know why so few of these transcripts, especially the ones selected from the cDNA library lists, turned out not to be significant differentially regulated between the two fish groups according to the RT-qPCR analyses. The reason for the observed discrepancy for some of the transcripts may rely on a number of inherent aspects with two methods, e.g. normalization procedures. Spearman rank correlation was used to search for possible co-variation in transcriptional levels of the 17 targets genes based on the RT-qPCR data, and for possible size-dependent transcriptional tendencies. No strong correlations were observed among the 17 studied target genes. Neither did any of the analyzed transcripts grouped distinctly together with one of the two dietary groups according to the Principal Component Analysis (PCA).


Exploring early micronutrient deficiencies in rainbow Trout (Oncorhynchus mykiss) by next-generation sequencing technology--from black box to functional genomics.

Olsvik PA, Hemre GI, Waagbø R - PLoS ONE (2013)

Significantly different expression of A) cyp1a3, and B) hmox1 in liver of rainbow trout fed diets with unsupplemented (Diet U) or supplemented (Diet S) levels of a vitamin and mineral premix.(Mean ± SEM). * P<0.05.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3722103&req=5

pone-0069461-g004: Significantly different expression of A) cyp1a3, and B) hmox1 in liver of rainbow trout fed diets with unsupplemented (Diet U) or supplemented (Diet S) levels of a vitamin and mineral premix.(Mean ± SEM). * P<0.05.
Mentions: Based on the findings from the SSH cDNA libraries, the transcriptional levels of a set of genes were determined with RT-qPCR from a total of 30 individual rainbow trout (15 fish from each dietary group). These genes were selected as potential markers of pathways suggested affected by the SSH cDNA libraries or as expected candidate biomarkers based on current knowledge. Table 3 lists the target genes selected for RT-qPCR verification. Only two out of 17 evaluated transcripts were significantly different between the two dietary groups (t-test). These were cyp1a3 (Figure 4A), and hmox1 (Figure 4B). We do at present not know why so few of these transcripts, especially the ones selected from the cDNA library lists, turned out not to be significant differentially regulated between the two fish groups according to the RT-qPCR analyses. The reason for the observed discrepancy for some of the transcripts may rely on a number of inherent aspects with two methods, e.g. normalization procedures. Spearman rank correlation was used to search for possible co-variation in transcriptional levels of the 17 targets genes based on the RT-qPCR data, and for possible size-dependent transcriptional tendencies. No strong correlations were observed among the 17 studied target genes. Neither did any of the analyzed transcripts grouped distinctly together with one of the two dietary groups according to the Principal Component Analysis (PCA).

Bottom Line: This work studies final nutritional status and transcriptional responses of rainbow trout (Oncorhynchus mykiss Walbaum 1792) (28 g) after a 10 week feeding experiment designed to elucidate the effect of adding a vitamin and mineral premix on growth, health, and nutritional endpoints.Processes related to lipid metabolism, peptide hydrolysis, oxygen transportation, and growth development were mostly affected.Considering the transcriptomics data relative to changes in nutritional status from the feeding study and the background phenotypic outcome of growth performance and gill histopathology, the outcome of the transcriptional profiling are suggested to be mainly related to suboptimal pantothenic acid and vitamin C nutrition.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Nutrition and Seafood Research (NIFES), Bergen, Norway. pal.olsvik@nifes.no

ABSTRACT
This work studies final nutritional status and transcriptional responses of rainbow trout (Oncorhynchus mykiss Walbaum 1792) (28 g) after a 10 week feeding experiment designed to elucidate the effect of adding a vitamin and mineral premix on growth, health, and nutritional endpoints. Juvenile fish were fed a either a diet supplemented with a vitamin and mineral premix (Diet S) or the same diet without premix supplementation (Diet U). The analyzed micronutrient composition of diets differed accordingly. Pooled livers from 15 fish from each dietary group were used to create suppression subtractive hybridization (SSH) cDNA libraries that were sequenced with 454 FLX GS Titanium Technology. In total 552 812 reads were sequenced from the two cDNA libraries. Ingenuity pathway analysis (IPA) was then used to characterize the hepatic transcriptome of the two dietary groups of rainbow trout. In the present communication we discuss how selected micronutrients may affect the transcriptome at suboptimal status by directly impacting the cellular metabolism, functions, and structures, and by introducing respective compensatory mechanisms. Processes related to lipid metabolism, peptide hydrolysis, oxygen transportation, and growth development were mostly affected. Considering the transcriptomics data relative to changes in nutritional status from the feeding study and the background phenotypic outcome of growth performance and gill histopathology, the outcome of the transcriptional profiling are suggested to be mainly related to suboptimal pantothenic acid and vitamin C nutrition.

Show MeSH
Related in: MedlinePlus