Project description:We report the application of Solexa/IlluminaM-bM-^@M-^Ys RNA-seq sequencing approaches for transcriptome in a marine fish under different conditions (bacterial- and mock-challenged conditions). By obtaining over four billion bases of sequence from the cDNA, we generated 169,950 none-redundant consensus sequences, from which 44842 functional transcripts with complete or various length of encoding regions were identified. More than 52% of these transcripts could be enriched in approximately 219 known metabolic or signaling pathways, among of which 2673 transcripts were found to be associated with immune-relevant genes. Besides, about 8% of the transcripts seemed fish-specific genes that have never been described before. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. Our study provided a global survey of the gene activities in host defense against bacterial infection in a non-model marine fish. Examination of different transcriptome in baterial- and mock challenged fish.

2012-08-09 | E-GEOD-21721 | biostudies-arrayexpress

Transcriptome profiling analysis of bacterial challenged Lateolabrax japonicus reveals deep insight into the immune-relevant genes in marine fish (RNA-seq)

Project description:We report the application of Solexa/Illumina’s RNA-seq sequencing approaches for transcriptome in a marine fish under different conditions (bacterial- and mock-challenged conditions). By obtaining over four billion bases of sequence from the cDNA, we generated 169,950 none-redundant consensus sequences, from which 44842 functional transcripts with complete or various length of encoding regions were identified. More than 52% of these transcripts could be enriched in approximately 219 known metabolic or signaling pathways, among of which 2673 transcripts were found to be associated with immune-relevant genes. Besides, about 8% of the transcripts seemed fish-specific genes that have never been described before. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. Our study provided a global survey of the gene activities in host defense against bacterial infection in a non-model marine fish.

2012-08-09 | GSE21721 | GEO

Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis.

Project description:Aliivibrio wodanis and Moritella viscosa have often been isolated together from fish with winter ulcer. Little is known about the interaction between the two bacterial species and how the presence of one bacterial species affects the behaviour of the other. The impact on bacterial growth in co-culture was investigated in vitro, and the presence of A. wodanis has a strong inhibitorial effect on M. viscosa. Further, we have sequenced the complete genomes of these two marine Gram-negative species, and have performed transcriptome analysis of the bacterial gene expression levels from in vivo samples. Using bacterial implants in the fish abdomen, we demonstrate that the presence of A. wodanis is altering the gene expression levels of M. viscosa compared to when the bacteria are implanted separately. The impeding effect on growth and the change in the global gene expression pattern of M. viscosa when the two pathogens co-exists is discussed in this paper.

2014-11-30 | E-MTAB-2851 | biostudies-arrayexpress

Novel fish pathogens of the Chlamydiae

Project description:Novel fish pathogens of the Chlamydiae

| PRJEB4490 | ENA

miRNA Characterization in Antarctic fish

Project description:miRNA Characterization in Antarctic fish

| PRJNA526522 | ENA

Genomic characterization of Listeria spp. from slaughterhouses, Spain

Project description:Genomic characterization of Listeria spp. from slaughterhouses, Spain

| PRJEB51772 | ENA

A nutritionally-enhanced oil from transgenic Camelina sativa effectively replaces marine fish oil as a source of eicosapentaenoic acid for farmed Atlantic salmon (Salmo salar)

Project description:The use of high levels of marine fish oil in aquafeeds is a non-sustainable practice. However, more sustainable oils sources from terrestrial plants do not contain long-chain polyunsaturated fatty acids (LC-PUFA). Consequently, feeds based on conventional vegetable oils reduce n-3 LC-PUFA levels in farmed fish. Therefore, the aquaculture industry desperately requires new, sustainable oil sources that contain high levels of n-3 LC-PUFA in order to supply the increasing demand for fish and seafood while maintaining the high nutritional quality of the farmed product. One approach to the renewable supply of n-3 LC-PUFA is metabolic engineering oilseed crops with the capacity to synthesize these essential fatty acids in seeds. In the present study, the oilseed Camelina sativa has been transformed with algal genes encoding the n-3 biosynthetic pathway and expression restricted to the seeds via seed-specific promoters to produce an oil containing > 20% eicosapentaenoic acid (EPA). This oil was investigated as a replacement for marine fish oil in feeds for post-smolt Atlantic salmon. In addition, this study with EPA-rich oil will contribute to our understanding of the biochemical and molecular mechanisms involved in the control and regulation of docosahexaenoic acid (DHA) production from EPA, and will thus better inform our understanding of this key part of the LC-PUFA biosynthetic pathway.

2015-12-21 | E-MTAB-2855 | biostudies-arrayexpress

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