1
|
Thambirajah AA, Miliano RC, Abbott EA, Buday C, Shang D, Kwok H, Helbing CC. Dynamic cyp1a1 transcript responses in the caudal fin of coho salmon (Oncorhynchus kisutch) smolts to low sulfur marine diesel water accommodated fraction exposures and depuration. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 256:106412. [PMID: 36716652 DOI: 10.1016/j.aquatox.2023.106412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Oil spills that occur in high traffic coastal environments can have profound consequences for the health of marine ecosystems and the commercial and social interests that are dependent upon these habitats. Given that the global reliance on marine fuels is not abating, it is imperative to develop sensitive and robust tools to monitor oil contamination and remediation in a timely manner. Such tools are increasingly important for ascertaining the immediate and long-term effects of oil contamination on species of interest and local habitats as water-soluble components of oils, such as polycyclic aromatic hydrocarbons (PAHs), can persist post-remediation. We previously demonstrated that 3-methylcholanthrene responsive cytochrome P450-1a (cyp1a1) transcript abundance in the liver and caudal fin of coho salmon smolts (Onchorhynchus kisutch) was sensitive to exposure to low sulfur marine diesel (LSMD) seawater accommodated fractions (seaWAF) in cold water. We expanded upon this paradigm by assessing the utility of the cyp1a1 transcript to track both exposure to LSMD seaWAF and recovery from exposure by measuring cyp1a1 abundance in coho smolts using quantitative polymerase chain reaction (qPCR). Smolts were exposed to either 100 mg/L LSMD seaWAF or clean seawater (control) for 4 days. Fish were then transferred to clean seawater for depuration and tissues sampled at 0, 1, 2, 4, and 8 days from both treatments. Livers and caudal fins were dissected from 40 smolts per group (ntotal = 400 smolts). The LSMD seaWAF-induced cyp1a1 transcript levels significantly decreased one day after depuration in the liver and caudal fin in a sex-independent manner in genotyped females and males. After four days of depuration, cyp1a1 transcript abundance decreased to baseline control levels, regardless of tissue or sex. The present study demonstrates the value of using the caudal fin as a reliable, sensitive, and non-lethal sampling and monitoring tool.
Collapse
Affiliation(s)
- Anita A Thambirajah
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Rachel C Miliano
- Pacific & Yukon Laboratory for Environmental Testing, Pacific Environmental Science Centre, Environment and Climate Change Canada, North Vancouver, British Columbia V7H 1B1, Canada
| | - Ethan A Abbott
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Craig Buday
- Pacific & Yukon Laboratory for Environmental Testing, Pacific Environmental Science Centre, Environment and Climate Change Canada, North Vancouver, British Columbia V7H 1B1, Canada
| | - Dayue Shang
- Pacific & Yukon Laboratory for Environmental Testing, Pacific Environmental Science Centre, Environment and Climate Change Canada, North Vancouver, British Columbia V7H 1B1, Canada
| | - Honoria Kwok
- Pacific & Yukon Laboratory for Environmental Testing, Pacific Environmental Science Centre, Environment and Climate Change Canada, North Vancouver, British Columbia V7H 1B1, Canada
| | - Caren C Helbing
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada.
| |
Collapse
|
2
|
Harshini V, Shukla N, Raval I, Kumar S, Shrivastava V, Patel AK, Joshi CG. Kidney transcriptome response to salinity adaptation in Labeo rohita. Front Physiol 2022; 13:991366. [PMID: 36311223 PMCID: PMC9606766 DOI: 10.3389/fphys.2022.991366] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
The increasing salinization of freshwater resources, owing to global warming, has caused concern to freshwater aquaculturists. In this regard, the present study is aimed at economically important freshwater fish, L. rohita (rohu) adapting to varying degrees of salinity concentrations. The RNA-seq analysis of kidney tissue samples of L. rohita maintained at 2, 4, 6, and 8 ppt salinity was performed, and differentially expressed genes involved in various pathways were studied. A total of 755, 834, 738, and 716 transcripts were downregulated and 660, 926, 576, and 908 transcripts were up-regulated in 2, 4, 6, and 8 ppt salinity treatment groups, respectively, with reference to the control. Gene ontology enrichment analysis categorized the differentially expressed genes into 69, 154, 92, and 157 numbers of biological processes with the p value < 0.05 for 2, 4, 6, and 8 ppt salinity groups, respectively, based on gene functions. The present study found 26 differentially expressed solute carrier family genes involved in ion transportation and glucose transportation which play a significant role in osmoregulation. In addition, the upregulation of inositol-3-phosphate synthase 1A (INO1) enzyme indicated the role of osmolytes in salinity acclimatization of L. rohita. Apart from this, the study has also found a significant number of genes involved in the pathways related to salinity adaptation including energy metabolism, calcium ion regulation, immune response, structural reorganization, and apoptosis. The kidney transcriptome analysis elucidates a step forward in understanding the osmoregulatory process in L. rohita and their adaptation to salinity changes.
Collapse
Affiliation(s)
- Vemula Harshini
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Nitin Shukla
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Ishan Raval
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Sujit Kumar
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, Gujarat, India
| | - Vivek Shrivastava
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, Gujarat, India
| | - Amrutlal K. Patel
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
- *Correspondence: Amrutlal K. Patel, ; Chaitanya G. Joshi,
| | - Chaitanya G. Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
- *Correspondence: Amrutlal K. Patel, ; Chaitanya G. Joshi,
| |
Collapse
|
3
|
Taugbøl A, Solbakken MH, Jakobsen KS, Vøllestad LA. Salinity-induced transcriptome profiles in marine and freshwater threespine stickleback after an abrupt 6-hour exposure. Ecol Evol 2022; 12:e9395. [PMID: 36311407 PMCID: PMC9596333 DOI: 10.1002/ece3.9395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Saltwater and freshwater environments have opposing physiological challenges, yet, there are fish species that are able to enter both habitats during short time spans, and as individuals they must therefore adjust quickly to osmoregulatory contrasts. In this study, we conducted an experiment to test for plastic responses to abrupt salinity changes in two populations of threespine stickleback, Gasterosteus aculeatus, representing two ecotypes (freshwater and ancestral saltwater). We exposed both ecotypes to abrupt native (control treatment) and non-native salinities (0‰ and 30‰) and sampled gill tissue for transcriptomic analyses after 6 h of exposure. To investigate genomic responses to salinity, we analyzed four different comparisons; one for each ecotype (in their control and exposure salinity; (1) and (2), one between ecotypes in their control salinity (3), and the fourth comparison included all transcripts identified in (3) that did not show any expressional changes within ecotype in either the control or the exposed salinity (4)). Abrupt salinity transfer affected the expression of 10 and 1530 transcripts for the saltwater and freshwater ecotype, respectively, and 1314 were differentially expressed between the controls, including 502 that were not affected by salinity within ecotype (fixed expression). In total, these results indicate that factors other than genomic expressional plasticity are important for osmoregulation in stickleback, due to the need for opposite physiological pathways to survive the abrupt change in salinity.
Collapse
Affiliation(s)
- Annette Taugbøl
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
- Norwegian Institute for Nature Research (NINA)LillehammerNorway
| | - Monica Hongrø Solbakken
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
| | - Kjetill S. Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
| | - Leif Asbjørn Vøllestad
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
| |
Collapse
|
4
|
Jiang JL, Xu J, Ye L, Sun ML, Jiang ZQ, Mao MG. Identification of differentially expressed genes in gills of tiger puffer (Takifugu rubripes) in response to low-salinity stress. Comp Biochem Physiol B Biochem Mol Biol 2020; 243-244:110437. [PMID: 32247057 DOI: 10.1016/j.cbpb.2020.110437] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/19/2020] [Accepted: 03/30/2020] [Indexed: 10/24/2022]
Abstract
Salinity is an important abiotic factor for aquatic organisms. In fish, changes in salinity affect physiological responses and alter the immune system. Takifugu rubripes is an important economic marine fish, and mechanisms of T. rubripes adaptation to salinity changes need to be further documented. In this study, a transcriptome sequencing technique was used to analyse genes that were differentially expressed in the T. rubripes gill after low-salinity stress for 30 d, and differential gene expression was further validated by quantitative real-time PCR (qPCR). After assembly, 385 differentially expressed genes (DEGs) were identified, including 182 upregulated genes and 203 downregulated genes. The DEGs were assigned to Gene Ontology (GO) classes with a total of 1647 functional terms. Most DEGs were assigned to biological process (984; 59.8%) followed by molecular function (445; 27.0%) and cellular component (218; 13.2%). Further KEGG analysis allocated 385 DEGs to 95 KEGG pathways. After q-value correction, 7 pathways (Glycolysis/Gluconeogenesis; Biosynthesis of amino acids; Carbon metabolism; Fructose and mannose metabolism; Pentose phosphate pathway; Metabolism of xenobiotics by cytochrome P450; and Glycine, serine and threonine metabolism) remained significant. qPCR results indicated that the transcripts of six selected genes sharply increased after 30 d of low-salinity stress. Low-salinity stress obviously increased SLC39A6, SLC5A9, NKAα1, CYP1A1, CYP1B1, and GSTA expression. In contrast, the genes encoding Aldoaa, GPI, FBP2 and GAPDH exhibited downregulation. In addition, three solute carrier (SLC) genes selected from the DEGs were further studied for differential expression patterns after low-salinity exposure, and the results showed that the SLCs were upregulated in T. rubripes after 72 h of low-salinity exposure. This investigation provides data for understanding the molecular mechanisms of fish responses to low-salinity stress and provides a reference for rationally setting salinity levels in aquaculture.
Collapse
Affiliation(s)
- Jie-Lan Jiang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Jia Xu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Lin Ye
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Meng-Lei Sun
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Zhi-Qiang Jiang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Ming-Guang Mao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China.
| |
Collapse
|
5
|
Alderman SL, Dilkumar CM, Avey SR, Farrell AP, Kennedy CJ, Gillis TE. Effects of diluted bitumen exposure and recovery on the seawater acclimation response of Atlantic salmon smolts. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 221:105419. [PMID: 32014643 DOI: 10.1016/j.aquatox.2020.105419] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 06/10/2023]
Abstract
Petrogenic chemicals are common and widespread contaminants in the aquatic environment. In Canada, increased extraction of bitumen from the oil sands and transport of the major crude oil export product, diluted bitumen (dilbit), amplifies the risk of a spill and contamination of Canadian waterways. Fish exposed to sublethal concentrations of crude oil can experience a variety of adverse physiological effects including osmoregulatory dysfunction. As regulation of water and ion balance is crucial during the seawater transition of anadromous fish, the hypothesis that dilbit impairs seawater acclimation in Atlantic salmon smolts (a fish at risk of exposure in Canada) was tested. Smolts were exposed for 24 d to the water-soluble fraction of dilbit in freshwater, and then transferred directly to seawater or allowed a 1 wk depuration period in uncontaminated freshwater prior to seawater transfer. The seawater acclimation response was quantified at 1 and 7 d post-transfer using established hematological, tissue, and molecular endpoints including gill Na+/K+-ATPase gene expression (nka). All smolts, irrespective of dilbit exposure, increased serum Na+ concentrations and osmolality within 1 d of seawater transfer. The recovery of these parameters to freshwater values by 7 d post-transfer was likely driven by the increased expression and activity of Na+/K+-ATPase in the gill. Histopathological changes in the gill were not observed; however, CYP1A-like immunoreactivity was detected in the pillar cells of gill lamellae of fish exposed to 67.9 μg/L PAC. Concentration-specific changes in kidney expression of a transmembrane water channel, aquaporin 3, occurred during seawater acclimation, but were resolved with 1 wk of depuration and were not associated with histopathological changes. In conclusion, apart from a robust CYP response in the gill, dilbit exposure did not greatly impact common measures of seawater acclimation, suggesting that significant osmoregulatory dysfunction is unlikely to occur if Atlantic salmon smolts are exposed sub-chronically to dilbit.
Collapse
Affiliation(s)
- Sarah L Alderman
- Department of Integrative Biology, University of Guelph, Ontario, Canada.
| | | | - Sean R Avey
- Department of Integrative Biology, University of Guelph, Ontario, Canada
| | - Anthony P Farrell
- Department of Zoology and Faculty of Land and Food Systems, University of British Columbia, British Columbia, Canada
| | - Christopher J Kennedy
- Department of Biological Sciences, Simon Fraser University, British Columbia, Canada
| | - Todd E Gillis
- Department of Integrative Biology, University of Guelph, Ontario, Canada
| |
Collapse
|
6
|
Schmitz M, Ziv T, Admon A, Baekelandt S, Mandiki SN, L'Hoir M, Kestemont P. Salinity stress, enhancing basal and induced immune responses in striped catfish Pangasianodon hypophthalmus (Sauvage). J Proteomics 2017; 167:12-24. [DOI: 10.1016/j.jprot.2017.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 12/12/2022]
|
7
|
Evaluation of potential candidate genes involved in salinity tolerance in striped catfish (Pangasianodon hypophthalmus) using an RNA-Seq approach. Mar Genomics 2015; 25:75-88. [PMID: 26653845 DOI: 10.1016/j.margen.2015.11.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/21/2015] [Accepted: 11/21/2015] [Indexed: 12/19/2022]
Abstract
Increasing salinity levels in freshwater and coastal environments caused by sea level rise linked to climate change is now recognized to be a major factor that can impact fish growth negatively, especially for freshwater teleost species. Striped catfish (Pangasianodon hypophthalmus) is an important freshwater teleost that is now widely farmed across the Mekong River Delta in Vietnam. Understanding the basis for tolerance and adaptation to raised environmental salinity conditions can assist the regional culture industry to mitigate predicted impacts of climate change across this region. Attempt of next generation sequencing using the ion proton platform results in more than 174 million raw reads from three tissue libraries (gill, kidney and intestine). Reads were filtered and de novo assembled using a variety of assemblers and then clustered together to generate a combined reference transcriptome. Downstream analysis resulted in a final reference transcriptome that contained 60,585 transcripts with an N50 of 683 bp. This resource was further annotated using a variety of bioinformatics databases, followed by differential gene expression analysis that resulted in 3062 transcripts that were differentially expressed in catfish samples raised under two experimental conditions (0 and 15 ppt). A number of transcripts with a potential role in salinity tolerance were then classified into six different functional gene categories based on their gene ontology assignments. These included; energy metabolism, ion transportation, detoxification, signal transduction, structural organization and detoxification. Finally, we combined the data on functional salinity tolerance genes into a hypothetical schematic model that attempted to describe potential relationships and interactions among target genes to explain the molecular pathways that control adaptive salinity responses in P. hypophthalmus. Our results indicate that P. hypophthalmus exhibit predictable plastic regulatory responses to elevated salinity by means of characteristic gene expression patterns, providing numerous candidate genes for future investigations.
Collapse
|
8
|
Leguen I, Le Cam A, Montfort J, Peron S, Fautrel A. Transcriptomic Analysis of Trout Gill Ionocytes in Fresh Water and Sea Water Using Laser Capture Microdissection Combined with Microarray Analysis. PLoS One 2015; 10:e0139938. [PMID: 26439495 PMCID: PMC4595143 DOI: 10.1371/journal.pone.0139938] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/18/2015] [Indexed: 12/22/2022] Open
Abstract
Fish gills represent a complex organ composed of several cell types that perform multiple physiological functions. Among these cells, ionocytes are implicated in the maintenance of ion homeostasis. However, because the ionocyte represents only a small percent of whole gill tissue, its specific transcriptome can be overlooked among the numerous cell types included in the gill. The objective of this study is to better understand ionocyte functions by comparing the RNA expression of this cell type in freshwater and seawater acclimated rainbow trout. To realize this objective, ionocytes were captured from gill cryosections using laser capture microdissection after immunohistochemistry. Then, transcriptome analyses were performed on an Agilent trout oligonucleotide microarray. Gene expression analysis identified 108 unique annotated genes differentially expressed between freshwater and seawater ionocytes, with a fold change higher than 3. Most of these genes were up-regulated in freshwater cells. Interestingly, several genes implicated in ion transport, extracellular matrix and structural cellular proteins appeared up-regulated in freshwater ionocytes. Among them, several ion transporters, such as CIC2, SLC26A6, and NBC, were validated by qPCR and/or in situ hybridization. The latter technique allowed us to localize the transcripts of these ion transporters in only ionocytes and more particularly in the freshwater cells. Genes involved in metabolism and also several genes implicated in transcriptional regulation, cell signaling and the cell cycle were also enhanced in freshwater ionocytes. In conclusion, laser capture microdissection combined with microarray analysis allowed for the determination of the transcriptional signature of scarce cells in fish gills, such as ionocytes, and aided characterization of the transcriptome of these cells in freshwater and seawater acclimated trout.
Collapse
Affiliation(s)
- Isabelle Leguen
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
- * E-mail:
| | - Aurélie Le Cam
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
| | | | - Sandrine Peron
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
| | - Alain Fautrel
- INSERM UMR991, Rennes, France
- Université de Rennes 1 Plateforme H2P2, Biosit, Rennes, France
| |
Collapse
|
9
|
Prunet P, Øverli Ø, Douxfils J, Bernardini G, Kestemont P, Baron D. Fish welfare and genomics. FISH PHYSIOLOGY AND BIOCHEMISTRY 2012; 38:43-60. [PMID: 21671026 DOI: 10.1007/s10695-011-9522-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 05/31/2011] [Indexed: 05/30/2023]
Abstract
There is a considerable public and scientific debate concerning welfare of fish in aquaculture. In this review, we will consider fish welfare as an integration of physiological, behavioral, and cognitive/emotional responses, all of which are essentially adaptative responses to stressful situations. An overview of fish welfare in this context suggests that understanding will rely on knowledge of all components of allostatic responses to stress and environmental perturbations. The development of genomic technologies provides new approaches to this task, exemplified by how genome-wide analysis of genetic structures and corresponding expression patterns can lead to the discovery of new aspects of adaptative responses. We will illustrate how the genomic approach may give rise to new biomarkers for fish welfare and also increase our understanding of the interaction between physiological, behavioral, and emotional responses. In a first part, we present data on expression of candidate genes selected a priori. This is a common avenue to develop molecular biomarkers capable of diagnosing a stress condition at its earliest onset, in order to allow quick corrective intervention in an aquaculture setting. However, most of these studies address isolated physiological functions and stress responses that may not be truly indicative of animal welfare, and there is only rudimentary understanding of genes related to possible cognitive and emotional responses in fish. We also present an overview on transcriptomic analysis related to the effect of aquaculture stressors, environmental changes (temperature, salinity, hypoxia), or concerning specific behavioral patterns. These studies illustrate the potential of genomic approaches to characterize the complexity of the molecular mechanisms which underlies not only physiological but also behavioral responses in relation to fish welfare. Thirdly, we address proteomic studies on biological responses to stressors such as salinity change and hypoxia. We will also consider proteomic studies developed in mammals in relation to anxiety and depressive status which may lead to new potential candidates in fish. Finally, in the conclusion, we will suggest new developments to facilitate an integrated view of fish welfare. This includes use of laser microdissection in the transcriptomic/proteomic studies, development of meta-analysis methods for extracting information from genomic data sets, and implementation of technological advances for high-throughput proteomic studies. Development of these new approaches should be as productive for our understanding of the biological processes underlying fish welfare as it has been for the progress of pathophysiological research.
Collapse
Affiliation(s)
- P Prunet
- UR1037 SCRIBE, IFR140, INRA, Campus de Beaulieu, Rennes, France.
| | | | | | | | | | | |
Collapse
|
10
|
Baron D, Dubois E, Bihouée A, Teusan R, Steenman M, Jourdon P, Magot A, Péréon Y, Veitia R, Savagner F, Ramstein G, Houlgatte R. Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns. BMC Genomics 2011; 12:113. [PMID: 21324190 PMCID: PMC3049149 DOI: 10.1186/1471-2164-12-113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 02/16/2011] [Indexed: 12/12/2022] Open
Abstract
Background DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid accumulation of muscle microarray data, it is of great interest to understand how to compare and combine data across multiple studies. Meta-analysis of transcriptome data is a valuable method to achieve it. It enables to highlight conserved gene signatures between multiple independent studies. However, using it is made difficult by the diversity of the available data: different microarray platforms, different gene nomenclature, different species studied, etc. Description We have developed a system tool dedicated to muscle transcriptome data. This system comprises a collection of microarray data as well as a query tool. This latter allows the user to extract similar clusters of co-expressed genes from the database, using an input gene list. Common and relevant gene signatures can thus be searched more easily. The dedicated database consists in a large compendium of public data (more than 500 data sets) related to muscle (skeletal and heart). These studies included seven different animal species from invertebrates (Drosophila melanogaster, Caenorhabditis elegans) and vertebrates (Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus). After a renormalization step, clusters of co-expressed genes were identified in each dataset. The lists of co-expressed genes were annotated using a unified re-annotation procedure. These gene lists were compared to find significant overlaps between studies. Conclusions Applied to this large compendium of data sets, meta-analyses demonstrated that conserved patterns between species could be identified. Focusing on a specific pathology (Duchenne Muscular Dystrophy) we validated results across independent studies and revealed robust biomarkers and new pathways of interest. The meta-analyses performed with MADMuscle show the usefulness of this approach. Our method can be applied to all public transcriptome data.
Collapse
|