4.6 Article

RNA-Seq Analysis of the Growth Hormone Transgenic Female Triploid Atlantic Salmon (Salmo salar) Hepatic Transcriptome Reveals Broad Temperature-Mediated Effects on Metabolism and Other Biological Processes

Related references

Note: Only part of the references are listed.
Article Fisheries

A comparison of triploid and diploid Atlantic salmon (Salmo salar) performance and welfare under commercial farming conditions in Norway

Angelico Madaro et al.

Summary: This study compared the performance of diploid and triploid Atlantic salmon from four Norwegian aquaculture companies under commercial conditions, revealing that triploid salmon exhibited reduced survival, higher incidence of emaciated fish, and scored lower quality ratings during primary processing. Further research is needed to improve the welfare and performance of triploid salmon in commercial aquaculture operations.

JOURNAL OF APPLIED AQUACULTURE (2022)

Article Pharmacology & Pharmacy

Aspirin effects on platelet gene expression are associated with a paradoxical, increase in platelet function

Rachel A. Myers et al.

Summary: The study demonstrates a dose-independent effect of aspirin on the platelet transcriptome, potentially acting as an inhibitor of protein synthesis, and correlated with platelet function levels.

BRITISH JOURNAL OF CLINICAL PHARMACOLOGY (2022)

Article Fisheries

Vertebral deformities in interspecific diploid and triploid salmonid hybrids

Thomas W. K. Fraser et al.

Summary: This study evaluated vertebral deformities in salmonid interspecific hybrids over three separate year classes during the freshwater life stage. Some of the salmonids were triploidised. The research found that pressure-shocked triploids had higher rates of vertebral deformities compared to diploids, regardless of hybridisation, and observed spontaneous triploidy in certain groups in the third-year class.

JOURNAL OF FISH BIOLOGY (2021)

Article Fisheries

Polyploidy affects fillet yield, composition, and fatty acid profile in two-year old, female rainbow trout, Oncorhynchus mykiss

Jeremy L. Everson et al.

Summary: By comparing sterile triploid female rainbow trout, pressure-induced triploids, and fertile diploids, it was found that sterile triploids exhibited better growth rates, yields, and intramuscular fat content.

AQUACULTURE (2021)

Article Biotechnology & Applied Microbiology

Integrated analysis of the responses of a circRNA-miRNA-mRNA ceRNA network to heat stress in rainbow trout (Oncorhynchus mykiss) liver

Jinqiang Quan et al.

Summary: The study investigated the transcriptomic changes in rainbow trout under heat stress and identified a strong stress response at high temperatures. A ceRNA regulatory network was constructed, and target genes involved in metabolic processes, biological regulation, and response to stimuli were highly induced. Several important pathways related to heat stress were characterized, providing novel insights for the development of strategies to alleviate heat stress.

BMC GENOMICS (2021)

Article Biochemistry & Molecular Biology

Transcriptome analysis provides the first insight into the molecular basis of temperature plasticity in Banggai cardinalfish, Pterapogon kauderni

Yu Pan et al.

Summary: Transcriptome analysis of Banggai cardinalfish revealed significant gene expression changes in response to different temperatures, identifying 47 genes potentially related to temperature stress. This study provides valuable information for further research on temperature tolerance in Banggai cardinalfish.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS (2021)

Article Biology

Acclimation to warm temperatures has important implications for mitochondrial function in Atlantic salmon (Salmo salar)

Lucie Gerber et al.

Summary: Acclimation to 20 degrees Celsius can protect the cardiac mitochondrial function of Atlantic salmon, decrease ROS production, and improve membrane integrity, but the plasticity may be limited when combined with other stressors.

JOURNAL OF EXPERIMENTAL BIOLOGY (2021)

Article Environmental Sciences

DNA Methylation Dynamics in Atlantic Salmon (Salmo salar) Challenged With High Temperature and Moderate Hypoxia

Anne Beemelmanns et al.

Summary: The study shows that exposure to high temperature or a combination of high temperature and hypoxia can induce changes in DNA methylation in Atlantic salmon. Different environmental conditions may lead to distinct epigenetic signatures, which are closely related to the duration of stress exposure.

FRONTIERS IN MARINE SCIENCE (2021)

Article Fisheries

Snow crab (Chionoecetes opilio) hepatopancreas transcriptome: Identification and testing of candidate molecular biomarkers of seismic survey impact

Jennifer R. Hall et al.

Summary: This study conducted field research on the eastern slope of the Grand Banks in Newfoundland and Labrador, Canada, investigating the potential impact of seismic exploration on the transcriptome of snow crab hepatopancreas. Differential expression analysis identified several transcripts with significant changes in response to seismic exposure, leading to the discovery of potential molecular biomarkers. Functional annotations of candidate seismic-responsive genes included oxidoreductase activity, apoptotic process, and inflammatory response.

FISHERIES RESEARCH (2021)

Article Biology

The effect of acute heat stress on the innate immune function of rainbow trout based on the transcriptome

Chang-Qing Zhou et al.

Summary: Research on the effects of acute heat stress on the innate immune function of rainbow trout identified differentially regulated mRNA, miRNA, and lncRNA, revealing specific regulatory mechanisms in the study.

JOURNAL OF THERMAL BIOLOGY (2021)

Article Multidisciplinary Sciences

Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar)

Ryan Brown et al.

Summary: This study compared the skin and gill microbiome of diploid and triploid Atlantic salmon, finding that ploidy can impact the microbial composition of the gills but not the skin-associated microbiome. Diploid salmon infected with SAV3 showed greater histopathological signs of epitheliocystis compared to triploid fish. The results suggest that ploidy may play a role in Atlantic salmon gill health and provide insights into co-infection with SAV3 and C. Branchiomonas.

PLOS ONE (2021)

Article Biotechnology & Applied Microbiology

The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

Anne Beemelmanns et al.

Summary: Increasing temperature to 20 degrees C alone, and in combination with hypoxia, resulted in differential expression of genes involved in similar pathways in Atlantic salmon. However, heat shock and immune-related genes in fish exposed to 20 degrees C and hypoxia were more affected, and strongly related to phenotypic characteristics such as growth. This study provides valuable information on how environmental challenges affect the expression of stress-, metabolic- and immune-related genes in fish, identifying potential biomarker genes for fish health and welfare improvement.

BMC GENOMICS (2021)

Article Fisheries

Comparative transcriptomic analysis brings new insights into the response to acute temperature acclimation in burbot (Lota lota lota)

Tianyan Yang et al.

Summary: This study used RNA sequencing to reveal gene expression differences in L. lota lota fish at different temperatures, finding more temperature-responsive genes in the high-temperature groups. HSP70 was identified as an effective biomarker for high-temperature challenges, while the upregulation of FAD could regulate fatty acid composition. Elevated temperature had a significant impact on the immune function of L. lota lota, potentially upregulating immune-related pathways.

AQUACULTURE REPORTS (2021)

Article Genetics & Heredity

The Atlantic salmon's stress- and immune-related transcriptional responses to moderate hypoxia, an incremental temperature increase, and these challenges combined

Anne Beemelmanns et al.

Summary: The study found that moderate hypoxia had an impact on the expression of stress genes at 12 degrees Celsius, while the effect of high temperature on these genes increased with rising temperatures. Long-term exposure to 20 degrees Celsius, with or without hypoxia, resulted in a limited acclimatory response in salmon. Additionally, immune-related genes were significantly affected at 20 degrees Celsius, especially when exposed to hypoxia challenge.

G3-GENES GENOMES GENETICS (2021)

Article Marine & Freshwater Biology

Incidence of skeletal deformities in induced triploid rainbow trout Oncorhynchus mykiss (Walbaum, 1792)

Krzysztof Jagiello et al.

Summary: Comparing the body abnormalities in diploid and triploid 14-month-old rainbow trout from commercial stocks, this research found a higher proportion of externally observed body deformities in triploid specimens, including spine deformities such as compressions and fusions of vertebrae. These abnormalities, though non-lethal, may negatively impact the condition and aesthetics of the fish, leading to potential economic losses in commercial production.

OCEANOLOGICAL AND HYDROBIOLOGICAL STUDIES (2021)

Article Biochemistry & Molecular Biology

RNA-seq reveals temporal differences in the transcriptome response to acute heat stress in the Atlantic salmon (Salmo salar)

Kun-Peng Shi et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS (2019)

Review Biochemical Research Methods

Understanding sequencing data as compositions: an outlook and review

Thomas P. Quinn et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Enis Afgan et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biotechnology & Applied Microbiology

Developing specific molecular biomarkers for thermal stress in salmonids

Arash Akbarzadeh et al.

BMC GENOMICS (2018)

Review Biochemistry & Molecular Biology

The Role of Peroxiredoxin 6 in Cell Signaling

Jose A. Arevalo et al.

ANTIOXIDANTS (2018)

Article Multidisciplinary Sciences

Impact of Salmonid alphavirus infection in diploid and triploid Atlantic salmon (Salmo salar L.) fry

Tharangani K. Herath et al.

PLOS ONE (2017)

Review Medicine, Research & Experimental

Recent progress in the research of cold-inducible RNA-binding protein

Peng Zhong et al.

FUTURE SCIENCE OA (2017)

Article Biochemistry & Molecular Biology

Triploid Atlantic salmon shows similar performance, fatty acid composition and proteome response to diploids during early freshwater rearing

Waldo G. Nuez-Ortin et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS (2017)

Article Biochemistry & Molecular Biology

Erythrocyte heat shock protein responses to chronic (in vivo) and acute (in vitro) temperature challenge in diploid and triploid salmonids

Pillai V. Saranyan et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY (2017)

Article Biochemistry & Molecular Biology

What do we not know about mitochondrial potassium channels?

Michal Laskowski et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2016)

Article Multidisciplinary Sciences

The Atlantic salmon genome provides insights into rediploidization

Sigbjorn Lien et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

Atlantic salmon (Salmo salar) liver transcriptome response to diets containing Camelina sativa products

Xi Xue et al.

Comparative Biochemistry and Physiology D-Genomics & Proteomics (2015)

Article Genetics & Heredity

Transcriptional Response to Acute Thermal Exposure in Juvenile Chinook Salmon Determined by RNAseq

Katharine M. H. Tomalty et al.

G3-GENES GENOMES GENETICS (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Evolutionary Biology

Transcriptomic responses to high water temperature in two species of Pacific salmon

Ken M. Jeffries et al.

EVOLUTIONARY APPLICATIONS (2014)

Article Biochemistry & Molecular Biology

Effect ofsevere environmental thermal stress on redox state in salmon

Toshiki Nakano et al.

REDOX BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

The effects of dissolved oxygen and triploidy on critical thermal maximum in brook charr (Salvelinus fontinalis)

Lauren E. Ellis et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY (2013)

Article Biochemistry & Molecular Biology

Family-specific differences in growth rate and hepatic gene expression in juvenile triploid growth hormone (GH) transgenic Atlantic salmon (Salmo salar)

Qingheng Xu et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS (2013)

Article Physiology

GH-IGF system regulation of attenuated muscle growth and lipolysis in Atlantic salmon reared at elevated sea temperatures

Ernst M. Hevroy et al.

JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMS AND ENVIRONMENTAL PHYSIOLOGY (2013)

Article Biochemical Research Methods

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

Jian Ye et al.

BMC BIOINFORMATICS (2012)

Review Biochemistry & Molecular Biology

Peroxiredoxin 6: A Bifunctional Enzyme with Glutathione Peroxidase and Phospholipase A2 Activities

Aron B. Fisher

ANTIOXIDANTS & REDOX SIGNALING (2011)

Article Biochemical Research Methods

Identification of novel transcripts in annotated genomes using RNA-Seq

Adam Roberts et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

BigWig and BigBed: enabling browsing of large distributed datasets

W. J. Kent et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

Eran Eden et al.

BMC BIOINFORMATICS (2009)

Article Biotechnology & Applied Microbiology

Highly Unsaturated Fatty Acid Synthesis in Atlantic Salmon: Characterization of ELOVL5-and ELOVL2-like Elongases

Sofia Morais et al.

MARINE BIOTECHNOLOGY (2009)

Article Biochemistry & Molecular Biology

Effect of acclimation temperature on routine metabolic rate in triploid salmonids

Michelle E. Atkins et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY (2008)

Article Biochemical Research Methods

Discovering motifs in ranked lists of DNA sequences

Eran Eden et al.

PLOS COMPUTATIONAL BIOLOGY (2007)

Article Fisheries

Response of fish membranes to environmental temperature

T Farkas et al.

AQUACULTURE RESEARCH (2001)

Article Biochemistry & Molecular Biology

A new mathematical model for relative quantification in real-time RT-PCR

MW Pfaffl

NUCLEIC ACIDS RESEARCH (2001)