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Rajab SAS, Andersen LK, Kenter LW, Berlinsky DL, Borski RJ, McGinty AS, Ashwell CM, Ferket PR, Daniels HV, Reading BJ. Combinatorial metabolomic and transcriptomic analysis of muscle growth in hybrid striped bass (female white bass Morone chrysops x male striped bass M. saxatilis). BMC Genomics 2024; 25:580. [PMID: 38858615 PMCID: PMC11165755 DOI: 10.1186/s12864-024-10325-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 04/19/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Understanding growth regulatory pathways is important in aquaculture, fisheries, and vertebrate physiology generally. Machine learning pattern recognition and sensitivity analysis were employed to examine metabolomic small molecule profiles and transcriptomic gene expression data generated from liver and white skeletal muscle of hybrid striped bass (white bass Morone chrysops x striped bass M. saxatilis) representative of the top and bottom 10 % by body size of a production cohort. RESULTS Larger fish (good-growth) had significantly greater weight, total length, hepatosomatic index, and specific growth rate compared to smaller fish (poor-growth) and also had significantly more muscle fibers of smaller diameter (≤ 20 µm diameter), indicating active hyperplasia. Differences in metabolomic pathways included enhanced energetics (glycolysis, citric acid cycle) and amino acid metabolism in good-growth fish, and enhanced stress, muscle inflammation (cortisol, eicosanoids) and dysfunctional liver cholesterol metabolism in poor-growth fish. The majority of gene transcripts identified as differentially expressed between groups were down-regulated in good-growth fish. Several molecules associated with important growth-regulatory pathways were up-regulated in muscle of fish that grew poorly: growth factors including agt and agtr2 (angiotensins), nicotinic acid (which stimulates growth hormone production), gadd45b, rgl1, zfp36, cebpb, and hmgb1; insulin-like growth factor signaling (igfbp1 and igf1); cytokine signaling (socs3, cxcr4); cell signaling (rgs13, rundc3a), and differentiation (rhou, mmp17, cd22, msi1); mitochondrial uncoupling proteins (ucp3, ucp2); and regulators of lipid metabolism (apoa1, ldlr). Growth factors pttg1, egfr, myc, notch1, and sirt1 were notably up-regulated in muscle of good-growing fish. CONCLUSION A combinatorial pathway analysis using metabolomic and transcriptomic data collectively suggested promotion of cell signaling, proliferation, and differentiation in muscle of good-growth fish, whereas muscle inflammation and apoptosis was observed in poor-growth fish, along with elevated cortisol (an anti-inflammatory hormone), perhaps related to muscle wasting, hypertrophy, and inferior growth. These findings provide important biomarkers and mechanisms by which growth is regulated in fishes and other vertebrates as well.
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Affiliation(s)
- Sarah A S Rajab
- Department of Applied Ecology, North Carolina State University, 100 Eugene Brooks Avenue, Box 7617, Raleigh, NC, 27695, USA
| | - Linnea K Andersen
- Department of Applied Ecology, North Carolina State University, 100 Eugene Brooks Avenue, Box 7617, Raleigh, NC, 27695, USA
| | - Linas W Kenter
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA
| | - David L Berlinsky
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA
| | - Russell J Borski
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Andrew S McGinty
- North Carolina State University, Pamlico Aquaculture Field Laboratory, Aurora, NC, USA
| | - Christopher M Ashwell
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Peter R Ferket
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Harry V Daniels
- Department of Applied Ecology, North Carolina State University, 100 Eugene Brooks Avenue, Box 7617, Raleigh, NC, 27695, USA
| | - Benjamin J Reading
- Department of Applied Ecology, North Carolina State University, 100 Eugene Brooks Avenue, Box 7617, Raleigh, NC, 27695, USA.
- North Carolina State University, Pamlico Aquaculture Field Laboratory, Aurora, NC, USA.
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Ma Y, Chen Y, Li Y, Chen S, Zhu C, Liu Q, Li L, Cao H, Wu Z, Dong W. Seasonal modulation of the testis transcriptome reveals insights into hibernation and reproductive adaptation in Onychostoma macrolepis. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024:10.1007/s10695-024-01335-4. [PMID: 38649597 DOI: 10.1007/s10695-024-01335-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024]
Abstract
The Onychostoma macrolepis have a unique survival strategy, overwintering in caves and returning to the river for reproduction in summer. The current knowledge on the developmental status of its testes during winter and summer is still undiscovered. We performed RNA-seq analysis on O. macrolepis testes between January and June, using the published genome (NCBI, ASM1243209v1). Through KEGG and GO enrichment analysis, we were able to identify 2111 differentially expressed genes (DEGs) and demonstrate their functions in signaling networks associated with the development of organism. At the genomic level, we found that during the overwintering phase, genes associated with cell proliferation (ccnb1, spag5, hdac7) were downregulated while genes linked to testicular fat metabolism (slc27a2, scd, pltp) were upregulated. This indicates suppression of both mitosis and meiosis, thereby inhibiting energy expenditure through genetic regulation of testicular degeneration. Furthermore, in January, we observed the regulation of autophagy and apoptosis (becn1, casp13), which may have the function of protecting reproductive organs and ensuring their maturity for the breeding season. The results provide a basis for the development of specialized feed formulations to regulate the expression of specific genes, or editing of genes during the fish egg stage, to ensure that the testes of O. macrolepis can mature more efficiently after overwintering, thereby enhancing reproductive performance.
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Affiliation(s)
- Yuxuan Ma
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yining Chen
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yan Li
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shaoxian Chen
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chao Zhu
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qimin Liu
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Long Li
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Heran Cao
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zifang Wu
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Wuzi Dong
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China.
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Zhou J, Sun S, Li R, Xu H, Li M, Li Z. Transcriptome analysis of Schizothorax oconnori (Cypriniformes: Cyprinidae) oocytes: The role of K + in promoting yolk globule fusion and regulating oocyte maturation. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:435-448. [PMID: 38047980 DOI: 10.1007/s10695-023-01272-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/12/2023] [Indexed: 12/05/2023]
Abstract
Schizothorax oconnori (S. oconnori) is an economically important fish in Tibet. Oocyte maturation is a physiological process that is of great significance to reproduction and seed production in S. oconnori, yet little is currently known regarding the molecular mechanisms of oocyte development in this species. To identify candidate genes involved in reproduction of female fish, a combination of PacBio and Illumina HiSeq technologies was employed to provide deep coverage of the oocyte transcriptome. Transcriptome analysis revealed several candidate genes that are potentially involved in the regulation of oocyte maturation in S. oconnori, including GIRK1, CHRM3, NPY2R, GABRA3, GnRH3, mGluR1α, GPER1, GDF9, HSP90, and ESR2. Genes that are significantly expressed during oocyte maturation mainly contribute to the GPCR signaling pathway and the estrogen signaling pathway. Neurotransmitter (Ach, NPY, and GABA) and peptide hormone (GnRH3) binding to G protein-coupled receptors (GPCRs) frees G-protein βγ subunits to interact with the G protein-gated inward rectifier K+ channel 1 (GIRK1). This process helps release K+ from granulosa cells to maturing oocytes, allowing yolk globule fusion. This mechanism may play an important role in oocyte maturation in S. oconnori. In conclusion, this study provides a valuable basis for deciphering the reproductive system in S. oconnori during the oocyte maturation process.
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Affiliation(s)
- Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850032, People's Republic of China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Province, Zhengzhou, 450046, People's Republic of China
| | - Shuaijie Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Province, Zhengzhou, 450046, People's Republic of China
| | - Ruiting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Province, Zhengzhou, 450046, People's Republic of China
| | - Huifeng Xu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Province, Zhengzhou, 450046, People's Republic of China
| | - Ming Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Province, Zhengzhou, 450046, People's Republic of China.
| | - Zhichao Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Province, Zhengzhou, 450046, People's Republic of China.
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Yang J, Lu B, Yu Z, Zhang L, Chen Y, Chen Z, Han C, Shu H. Multiple Tissues Transcriptome of Zig-Zag Eel ( Mastacembelus armatus) with Different Growth Rates. Animals (Basel) 2024; 14:248. [PMID: 38254417 PMCID: PMC10812625 DOI: 10.3390/ani14020248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
In order to explore the main regulatory genes and related pathways of growth traits, transcriptome sequencing was first performed on the brain, liver, and muscle tissues of 3-month-old M. armatus with different growth rates. By comparative transcriptome analysis of fast-growing and slow-growing groups of M. armatus, a total of 2887 DEGs were screened, of which 59 up-regulated genes and 105 down-regulated genes were detected in the brain, 146 up-regulated genes and 202 down-regulated genes were detected in the liver, and 529 up-regulated genes and 1846 down-regulated genes were detected in muscle, including insulin-like growth factor binding protein 1a (IGFBP1A), insulin-like growth factor binding protein 1b (IGFBP1B), myosin, light chain 1 (MYL1), and myoglobin (MB). Through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we identified a total of 288 significantly enriched GO entries and 68 significantly enriched KEGG pathways related to growth, such as skeletal muscle tissue development, insulin-like growth factor binding, and the mitotic cell cycle. These key genes and signaling pathways may play a key role in regulating the growth of M. armatus. Digging into the regulatory mechanisms of these key genes will provide a theoretical basis for further exploration of the molecular mechanisms related to the growth and development of M. armatus, and help to breed new varieties of M. armatus with rapid growth.
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Affiliation(s)
| | | | | | | | | | | | - Chong Han
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (J.Y.); (B.L.); (Z.Y.); (L.Z.); (Y.C.); (Z.C.)
| | - Hu Shu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (J.Y.); (B.L.); (Z.Y.); (L.Z.); (Y.C.); (Z.C.)
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5
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Newell AJ, Jima D, Reading B, Patisaul HB. Machine learning reveals common transcriptomic signatures across rat brain and placenta following developmental organophosphate ester exposure. Toxicol Sci 2023; 195:103-122. [PMID: 37399109 PMCID: PMC10695431 DOI: 10.1093/toxsci/kfad062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Abstract
Toxicogenomics is a critical area of inquiry for hazard identification and to identify both mechanisms of action and potential markers of exposure to toxic compounds. However, data generated by these experiments are highly dimensional and present challenges to standard statistical approaches, requiring strict correction for multiple comparisons. This stringency often fails to detect meaningful changes to low expression genes and/or eliminate genes with small but consistent changes particularly in tissues where slight changes in expression can have important functional differences, such as brain. Machine learning offers an alternative analytical approach for "omics" data that effectively sidesteps the challenges of analyzing highly dimensional data. Using 3 rat RNA transcriptome sets, we utilized an ensemble machine learning approach to predict developmental exposure to a mixture of organophosphate esters (OPEs) in brain (newborn cortex and day 10 hippocampus) and late gestation placenta of male and female rats, and identified genes that informed predictor performance. OPE exposure had sex specific effects on hippocampal transcriptome, and significantly impacted genes associated with mitochondrial transcriptional regulation and cation transport in females, including voltage-gated potassium and calcium channels and subunits. To establish if this holds for other tissues, RNAseq data from cortex and placenta, both previously published and analyzed via a more traditional pipeline, were reanalyzed with the ensemble machine learning methodology. Significant enrichment for pathways of oxidative phosphorylation and electron transport chain was found, suggesting a transcriptomic signature of OPE exposure impacting mitochondrial metabolism across tissue types and developmental epoch. Here we show how machine learning can complement more traditional analytical approaches to identify vulnerable "signature" pathways disrupted by chemical exposures and biomarkers of exposure.
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Affiliation(s)
- Andrew J Newell
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Dereje Jima
- Molecular Education, Technology, and Research Innovation Center, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Benjamin Reading
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Heather B Patisaul
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695, USA
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6
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Ocalewicz K. Quality of fish eggs and production of androgenetic and gynogenetic doubled haploids (DHs). FISH PHYSIOLOGY AND BIOCHEMISTRY 2023:10.1007/s10695-023-01206-4. [PMID: 37296321 DOI: 10.1007/s10695-023-01206-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/19/2023] [Indexed: 06/12/2023]
Abstract
Induced development of haploid embryos (H) with only paternal (androgenesis) or maternal (gynogenesis) chromosomes requires irradiation of eggs before fertilization or activation of eggs with irradiated spermatozoa, respectively. To provide doubled haploids (DHs), androgenetic and gynogenetic haploid zygotes need to be subjected to the thermal or high hydrostatic pressure (HHP) shock to suppress the first mitotic cleavage and to double paternal or maternal haploid set of chromosomes. Androgenesis and mitotic gynogenesis (mito-gynogenesis) result in the generation of fully homozygous individuals in a single generation. DHs have been utilized in selective breeding programs, in studies concerning the phenotypic consequences of recessive alleles and to evaluate the impact of sex chromosomes on the early ontogeny. Moreover, the use of DHs for the NGS approach radically improves de novo the assembly of the genomes. However, reduced survival of the doubled haploids limits the wide application of androgenotes and gynogenotes. The high mortality of DHs may be only partly explained by the expression of recessive traits. Observed inter-clutch variation in the survival of DHs developing in eggs originating from different females make it necessary to take a closer look at the quality of the eggs used during induced androgenesis and gynogenesis. Moreover, the developmental competence of eggs that are subjected to irradiation before fertilization in order to deactivate maternal chromosomes when undergoing induced androgenesis and exposed to the physical shock after fertilization that leads to the duplication of the zygotes in both mito-gynogenesis and androgenesis may be also altered as irradiation and sublethal values of temperatures and hydrostatic pressure are considered as harmful for the cell organelles and biomolecules. Here, recently provided results concerning the morphological, biochemical, genomic, and transcriptomic characteristics of fish eggs showing high and low competence for androgenesis and mito-gynogenesis are reviewed.
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Affiliation(s)
- Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, Al. M. Piłsudskiego 46, 81-378, Gdynia, Poland.
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7
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Nolin SJ, Taylor RL, Edens FW, Siegel PB, Ashwell CM. Combining supervised machine learning with statistics reveals differential gene expression patterns related to energy metabolism in the jejuna of chickens divergently selected for antibody response to sheep red blood cells. Poult Sci 2023; 102:102751. [PMID: 37244088 DOI: 10.1016/j.psj.2023.102751] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/19/2023] [Accepted: 04/23/2023] [Indexed: 05/29/2023] Open
Abstract
Since the 1970s, 2 lines of White Leghorn chickens, HAS and LAS, have been continuously divergently selected for 5-day postinjection antibody titer to injection with sheep red blood cells (SRBC). Antibody response is a complex genetic trait and characterizing differences in gene expression could facilitate better understanding of physiological changes due to selection and antigen exposure. At 41 d of age, randomly selected HAS and LAS chickens, which had been coraised from hatch, were either injected with SRBC (HASI and LASI) or kept as the noninjected cohort (HASN and LASN). Five days later, all were euthanized, and samples collected from the jejunum for RNA isolation and sequencing. Resulting gene expression data were analyzed combining traditional statistics with machine learning to obtain signature gene lists for functional analysis. Differences in ATP production and cellular processes were observed in the jejunum between lines and following SRBC injection. HASN vs. LASN exhibited upregulation of ATP production, immune cell motility, and inflammation. LASI exhibits upregulation of ATP production and protein synthesis vs. LASN, reflective of what was observed in HASN vs. LASN. In contrast, no corresponding upregulation of ATP production was observed in HASI vs. HASN, and most other cellular processes appear inhibited. Without exposure to SRBC, gene expression in the jejunum indicates HAS generates more ATP than LAS, suggesting HAS maintains a "primed" system; and gene expression of HASI vs. HASN further suggests this basal ATP production is sufficient for robust antibody responses. Conversely, LASI vs. LASN jejunal gene expression implies a physiological need for increased ATP production with only minimal correlating antibody production. The results of this experiment provide insight into energetic resource needs and allocations in the jejunum in response to genetic selection and antigen exposure in HAS and LAS which may help explain phenotypic differences observed in antibody response.
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Affiliation(s)
- Shelly J Nolin
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA.
| | - Robert L Taylor
- Davis College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown West, VA 26506-6108, USA
| | - Frank W Edens
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Paul B Siegel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Christopher M Ashwell
- Davis College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown West, VA 26506-6108, USA
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Giacomini JJ, Adler LS, Reading BJ, Irwin RE. Differential bumble bee gene expression associated with pathogen infection and pollen diet. BMC Genomics 2023; 24:157. [PMID: 36991318 DOI: 10.1186/s12864-023-09143-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/18/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Diet and parasitism can have powerful effects on host gene expression. However, how specific dietary components affect host gene expression that could feed back to affect parasitism is relatively unexplored in many wild species. Recently, it was discovered that consumption of sunflower (Helianthus annuus) pollen reduced severity of gut protozoan pathogen Crithidia bombi infection in Bombus impatiens bumble bees. Despite the dramatic and consistent medicinal effect of sunflower pollen, very little is known about the mechanism(s) underlying this effect. However, sunflower pollen extract increases rather than suppresses C. bombi growth in vitro, suggesting that sunflower pollen reduces C. bombi infection indirectly via changes in the host. Here, we analyzed whole transcriptomes of B. impatiens workers to characterize the physiological response to sunflower pollen consumption and C. bombi infection to isolate the mechanisms underlying the medicinal effect. B. impatiens workers were inoculated with either C. bombi cells (infected) or a sham control (un-infected) and fed either sunflower or wildflower pollen ad libitum. Whole abdominal gene expression profiles were then sequenced with Illumina NextSeq 500 technology. RESULTS Among infected bees, sunflower pollen upregulated immune transcripts, including the anti-microbial peptide hymenoptaecin, Toll receptors and serine proteases. In both infected and un-infected bees, sunflower pollen upregulated putative detoxification transcripts and transcripts associated with the repair and maintenance of gut epithelial cells. Among wildflower-fed bees, infected bees downregulated immune transcripts associated with phagocytosis and the phenoloxidase cascade. CONCLUSIONS Taken together, these results indicate dissimilar immune responses between sunflower- and wildflower-fed bumble bees infected with C. bombi, a response to physical damage to gut epithelial cells caused by sunflower pollen, and a strong detoxification response to sunflower pollen consumption. Identifying host responses that drive the medicinal effect of sunflower pollen in infected bumble bees may broaden our understanding of plant-pollinator interactions and provide opportunities for effective management of bee pathogens.
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Affiliation(s)
- Jonathan J Giacomini
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Lynn S Adler
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Benjamin J Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Rebecca E Irwin
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695, USA
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Cao H, Gao H, Li Z, Peng G, Chen Y, Jin T, Zhu C, Ji H, Dong W. Comparative transcriptome provides insights into differentially expressed genes between testis and ovary of Onychostoma macrolepis in reproduction period. Gen Comp Endocrinol 2022; 326:114066. [PMID: 35644279 DOI: 10.1016/j.ygcen.2022.114066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 04/28/2022] [Accepted: 05/22/2022] [Indexed: 11/28/2022]
Abstract
The Onychostoma macrolepis (O. macrolepis) is a rare and endangered fishery species inhabiting the river of Qinling Mountains and some flowing freshwaters in China. The declining population of O. macrolepis caused by asynchrony of male and female development prompted us to focus on genetic regulation of its reproduction. In this study, high-throughput RNA-sequencing technology was applied to assemble and annotate the transcriptome of O. macrolepis testis and ovary. The results showed that a number of 338089335 (ovary:163216500, testis:174872835) raw sequences were obtained. After non-redundant analysis, a number of 207826065 (ovary:102334008, testis:105492057) high quality reads were obtained and predicted as unigenes, in which 201,038,682 unigenes were annotated with multiple databases. Taking the ovarian transcriptome as a control, comparative transcriptome analysis showed that 9918 differentially expressed genes (DEGs) up-regulated in the testis and 13,095 DEGs down-regulated. Many DEGs were involved with sex-related GO terms and KEGG pathways, such as oocyte maturation, gonadal development, steroid biosynthesis pathways, MAPK signaling pathway and Wnt signaling pathway. Finally, the expression patterns of 19 unigenes were validated by using quantitative real-time polymerase chain reaction (qRT-PCR). This study illustrates a potential molecular mechanism on the unsynchronized male and female development of the O. macrolepis during the reproduction period in June and provides a theoretical basis for future artificial reproduction.
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Affiliation(s)
- Heran Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Huihui Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zhenpeng Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Guofan Peng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yining Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Tianqi Jin
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Chao Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hong Ji
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Wuzi Dong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Yilmaz O, Jensen AM, Harboe T, Møgster M, Jensen RM, Mjaavatten O, Birkeland E, Spriet E, Sandven L, Furmanek T, Berven FS, Wargelius A, Norberg B. Quantitative proteome profiling reveals molecular hallmarks of egg quality in Atlantic halibut: impairments of transcription and protein folding impede protein and energy homeostasis during early development. BMC Genomics 2022; 23:635. [PMID: 36071374 PMCID: PMC9450261 DOI: 10.1186/s12864-022-08859-0] [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: 02/15/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Background Tandem mass tag spectrometry (TMT labeling-LC-MS/MS) was utilized to examine the global proteomes of Atlantic halibut eggs at the 1-cell-stage post fertilization. Comparisons were made between eggs judged to be of good quality (GQ) versus poor quality (BQ) as evidenced by their subsequent rates of survival for 12 days. Altered abundance of selected proteins in BQ eggs was confirmed by parallel reaction monitoring spectrometry (PRM-LC-MS/MS). Correspondence of protein levels to expression of related gene transcripts was examined via qPCR. Potential mitochondrial differences between GQ and BQ eggs were assessed by transmission electron microscopy (TEM) and measurements of mitochondrial DNA (mtDNA) levels. Results A total of 115 proteins were found to be differentially abundant between GQ and BQ eggs. Frequency distributions of these proteins indicated higher protein folding activity in GQ eggs compared to higher transcription and protein degradation activities in BQ eggs. BQ eggs were also significantly enriched with proteins related to mitochondrial structure and biogenesis. Quantitative differences in abundance of several proteins with parallel differences in their transcript levels were confirmed in egg samples obtained over three consecutive reproductive seasons. The observed disparities in global proteome profiles suggest impairment of protein and energy homeostasis related to unfolded protein response and mitochondrial stress in BQ eggs. TEM revealed BQ eggs to contain significantly higher numbers of mitochondria, but differences in corresponding genomic mtDNA (mt-nd5 and mt-atp6) levels were not significant. Mitochondria from BQ eggs were significantly smaller with a more irregular shape and a higher number of cristae than those from GQ eggs. Conclusion The results of this study indicate that BQ Atlantic halibut eggs are impaired at both transcription and translation levels leading to endoplasmic reticulum and mitochondrial disorders. Observation of these irregularities over three consecutive reproductive seasons in BQ eggs from females of diverse background, age and reproductive experience indicates that they are a hallmark of poor egg quality. Additional research is needed to discover when in oogenesis and under what circumstances these defects may arise. The prevalence of this suite of markers in BQ eggs of diverse vertebrate species also begs investigation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08859-0.
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Affiliation(s)
- Ozlem Yilmaz
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway.
| | | | - Torstein Harboe
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
| | - Margareth Møgster
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
| | | | - Olav Mjaavatten
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Even Birkeland
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Endy Spriet
- Department of Biomedicine, The Molecular Imaging Center (MIC), University of Bergen, 5009, Bergen, Norway
| | - Linda Sandven
- Department of Biomedicine, The Molecular Imaging Center (MIC), University of Bergen, 5009, Bergen, Norway
| | - Tomasz Furmanek
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Anna Wargelius
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Birgitta Norberg
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
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11
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Nargesi EA, Falahatkar B, Żarski D. Artificial reproduction of Caspian roach, Rutilus caspicus following stimulating ovulation with Ovaprim, Ovopel, and their combinations under controlled conditions. Anim Reprod Sci 2022; 238:106932. [DOI: 10.1016/j.anireprosci.2022.106932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/18/2022]
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12
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Neurodevelopment vs. the immune system: Complementary contributions of maternally-inherited gene transcripts and proteins to successful embryonic development in fish. Genomics 2021; 113:3811-3826. [PMID: 34508856 DOI: 10.1016/j.ygeno.2021.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/12/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022]
Abstract
The aim of this study was to investigate the respective contribution of maternally-inherited mRNAs and proteins to egg molecular cargo and to its developmental competence in fish using pikeperch as a model. Our study provides novel insights into the understanding of type-specific roles of maternally-inherited molecules in fish. Here we show, for the first time, that transcripts and proteins have distinct, yet complementary, functions in the egg of teleost fish. Maternally-inherited mRNAs would shape embryo neurodevelopment, while maternally-inherited proteins would rather be responsible for protecting the embryo against pathogens. Additionally, we observed that processes directly preceding ovulation may considerably affect the reproductive success by modifying expression level of genes crucial for proper embryonic development, being novel fish egg quality markers (e.g., smarca4 or h3f3a). These results are of major importance for understanding the influence of external factors on reproductive fitness in both captive and wild-type fish species.
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13
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Weber GM, Birkett J, Martin K, Dixon D, Gao G, Leeds TD, Vallejo RL, Ma H. Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability. BMC Genomics 2021; 22:448. [PMID: 34130620 PMCID: PMC8207762 DOI: 10.1186/s12864-021-07773-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
Background Transcription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the mRNA required for oocyte maturation, fertilization, and early cleavage of the embryo. The transcriptome of the unfertilized egg, therefore, has potential to provide markers for predictors of egg quality and diagnosing problems with embryo production encountered by fish hatcheries. Although levels of specific transcripts have been shown to associate with measures of egg quality, these differentially expressed genes (DEGs) have not been consistent among studies. The present study compares differences in select transcripts among unfertilized rainbow trout eggs of different quality based on eyeing rate, among 2 year classes of the same line (A1, A2) and a population from a different hatchery (B). The study compared 65 transcripts previously reported to be differentially expressed with egg quality in rainbow trout. Results There were 32 transcripts identified as DEGs among the three groups by regression analysis. Group A1 had the most DEGs, 26; A2 had 15, 14 of which were shared with A1; and B had 12, 7 of which overlapped with A1 or A2. Six transcripts were found in all three groups, dcaf11, impa2, mrpl39_like, senp7, tfip11 and uchl1. Conclusions Our results confirmed maternal transcripts found to be differentially expressed between low- and high-quality eggs in one population of rainbow trout can often be found to overlap with DEGs in other populations. The transcripts differentially expressed with egg quality remain consistent among year classes of the same line. Greater similarity in dysregulated transcripts within year classes of the same line than among lines suggests patterns of transcriptome dysregulation may provide insight into causes of decreased viability within a hatchery population. Although many DEGs were identified, for each of the genes there is considerable variability in transcript abundance among eggs of similar quality and low correlations between transcript abundance and eyeing rate, making it highly improbable to predict the quality of a single batch of eggs based on transcript abundance of just a few genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07773-1.
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Affiliation(s)
- Gregory M Weber
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA.
| | - Jill Birkett
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | | | | | - Guangtu Gao
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | - Timothy D Leeds
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | - Roger L Vallejo
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | - Hao Ma
- USDA/ARS Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Ames, IA, USA
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14
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Vision-based egg quality prediction in Pacific bluefin tuna (Thunnus orientalis) by deep neural network. Sci Rep 2021; 11:6. [PMID: 33436861 PMCID: PMC7804258 DOI: 10.1038/s41598-020-80001-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/07/2020] [Indexed: 11/17/2022] Open
Abstract
Closed-cycle aquaculture using hatchery produced seed stocks is vital to the sustainability of endangered species such as Pacific bluefin tuna (Thunnus orientalis) because this aquaculture system does not depend on aquaculture seeds collected from the wild. High egg quality promotes efficient aquaculture production by improving hatch rates and subsequent growth and survival of hatched larvae. In this study, we investigate the possibility of a simple, low-cost, and accurate egg quality prediction system based only on photographic images using deep neural networks. We photographed individual eggs immediately after spawning and assessed their qualities, i.e., whether they hatched normally and how many days larvae survived without feeding. The proposed system predicted normally hatching eggs with higher accuracy than human experts. It was also successful in predicting which eggs would produce longer-surviving larvae. We also analyzed the image aspects that contributed to the prediction to discover important egg features. Our results suggest the applicability of deep learning techniques to efficient egg quality prediction, and analysis of early developmental stages of development.
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15
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Koutsouveli V, Cárdenas P, Santodomingo N, Marina A, Morato E, Rapp HT, Riesgo A. The Molecular Machinery of Gametogenesis in Geodia Demosponges (Porifera): Evolutionary Origins of a Conserved Toolkit across Animals. Mol Biol Evol 2020; 37:3485-3506. [PMID: 32929503 PMCID: PMC7743902 DOI: 10.1093/molbev/msaa183] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
All animals are capable of undergoing gametogenesis. The ability of forming haploid cells from diploid cells through meiosis and recombination appeared early in eukaryotes, whereas further gamete differentiation is mostly a metazoan signature. Morphologically, the gametogenic process presents many similarities across animal taxa, but little is known about its conservation at the molecular level. Porifera are the earliest divergent animals and therefore are an ideal phylum to understand evolution of the gametogenic toolkits. Although sponge gametogenesis is well known at the histological level, the molecular toolkits for gamete production are largely unknown. Our goal was to identify the genes and their expression levels which regulate oogenesis and spermatogenesis in five gonochoristic and oviparous species of the genus Geodia, using both RNAseq and proteomic analyses. In the early stages of both female and male gametogenesis, genes involved in germ cell fate and cell-renewal were upregulated. Then, molecular signals involved in retinoic acid pathway could trigger the meiotic processes. During later stages of oogenesis, female sponges expressed genes involved in cell growth, vitellogenesis, and extracellular matrix reassembly, which are conserved elements of oocyte maturation in Metazoa. Likewise, in spermatogenesis, genes regulating the whole meiotic cycle, chromatin compaction, and flagellum axoneme formation, that are common across Metazoa were overexpressed in the sponges. Finally, molecular signals possibly related to sperm capacitation were identified during late stages of spermatogenesis for the first time in Porifera. In conclusion, the activated molecular toolkit during gametogenesis in sponges was remarkably similar to that deployed during gametogenesis in vertebrates.
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Affiliation(s)
- Vasiliki Koutsouveli
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC, Uppsala, Sweden
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC, Uppsala, Sweden
| | - Nadiezhda Santodomingo
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
| | - Anabel Marina
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid (UAM) and Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Esperanza Morato
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid (UAM) and Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Hans Tore Rapp
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
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16
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Crisci E, Moroldo M, Vu Manh TP, Mohammad A, Jourdren L, Urien C, Bouguyon E, Bordet E, Bevilacqua C, Bourge M, Pezant J, Pléau A, Boulesteix O, Schwartz I, Bertho N, Giuffra E. Distinctive Cellular and Metabolic Reprogramming in Porcine Lung Mononuclear Phagocytes Infected With Type 1 PRRSV Strains. Front Immunol 2020; 11:588411. [PMID: 33365028 PMCID: PMC7750501 DOI: 10.3389/fimmu.2020.588411] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/19/2020] [Indexed: 01/17/2023] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) has an extensive impact on pig production. The causative virus (PRRSV) is divided into two species, PRRSV-1 (European origin) and PRRSV-2 (North American origin). Within PRRSV-1, PRRSV-1.3 strains, such as Lena, are more pathogenic than PRRSV-1.1 strains, such as Flanders 13 (FL13). To date, the molecular interactions of PRRSV with primary lung mononuclear phagocyte (MNP) subtypes, including conventional dendritic cells types 1 (cDC1) and 2 (cDC2), monocyte-derived DCs (moDC), and pulmonary intravascular macrophages (PIM), have not been thoroughly investigated. Here, we analyze the transcriptome profiles of in vivo FL13-infected parenchymal MNP subpopulations and of in vitro FL13- and Lena-infected parenchymal MNP. The cell-specific expression profiles of in vivo sorted cells correlated with their murine counterparts (AM, cDC1, cDC2, moDC) with the exception of PIM. Both in vivo and in vitro, FL13 infection altered the expression of a low number of host genes, and in vitro infection with Lena confirmed the higher ability of this strain to modulate host response. Machine learning (ML) and gene set enrichment analysis (GSEA) unraveled additional relevant genes and pathways modulated by FL13 infection that were not identified by conventional analyses. GSEA increased the cellular pathways enriched in the FL13 data set, but ML allowed a more complete comprehension of functional profiles during FL13 in vitro infection. Data indicates that cellular reprogramming differs upon Lena and FL13 infection and that the latter might keep antiviral and inflammatory macrophage/DC functions silent. Although the slow replication kinetics of FL13 likely contribute to differences in cellular gene expression, the data suggest distinct mechanisms of interaction of the two viruses with the innate immune system during early infection.
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Affiliation(s)
- Elisa Crisci
- Université Paris Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Marco Moroldo
- Université Paris Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Ammara Mohammad
- Genomics Core Facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Laurent Jourdren
- Genomics Core Facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Celine Urien
- Virologie et Immunologie Moléculaire, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Edwige Bouguyon
- Virologie et Immunologie Moléculaire, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Elise Bordet
- Virologie et Immunologie Moléculaire, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Claudia Bevilacqua
- Université Paris Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Mickael Bourge
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jérémy Pezant
- Plate-Forme d'Infectiologie Expérimentale-PFIE-UE1277, Centre Val de Loire, INRAE, Nouzilly, France
| | - Alexis Pléau
- Plate-Forme d'Infectiologie Expérimentale-PFIE-UE1277, Centre Val de Loire, INRAE, Nouzilly, France
| | - Olivier Boulesteix
- Plate-Forme d'Infectiologie Expérimentale-PFIE-UE1277, Centre Val de Loire, INRAE, Nouzilly, France
| | - Isabelle Schwartz
- Virologie et Immunologie Moléculaire, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nicolas Bertho
- Virologie et Immunologie Moléculaire, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Elisabetta Giuffra
- Université Paris Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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17
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Ma S, Li LH, Hao SX, Yang XQ, Huang H, Cen JW, Wang YQ. Fatty-acid Profiles and Fingerprints of Seven Types of Fish Roes as Determined by Chemometric Methods. J Oleo Sci 2020; 69:1199-1208. [PMID: 32908092 DOI: 10.5650/jos.ess20061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The fatty acids in seven species of fish roes were determined by GC-MS in combination with principal component and cluster analyses in order to derive their fatty-acid profiles and fingerprints. Twenty-three common chromatography peaks were identified in the fatty-acid fingerprints of the seven fish roes. A total of 19 typical fatty acids were identified in the fish roes studied. The fatty acid contents of the roes were significantly different, with saturated-fatty-acid contents in the seven roes ranging from 26.69% to 41.81%, and the unsaturated-fatty-acid contents ranging from 57.65% to 72.21%, the total EPA and DHA content (37.20%) is high in E. cypselurus roe, especially. The seven roe species were clearly distinguished according to fatty-acid composition and content by principal component analysis (PCA) and divided into two groups by cluster analysis (CA). PCA of the fatty acid data yielded three significant PCs , which together account for 94% of the total variance; with PC1 contributing 54% of the total.
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Affiliation(s)
- Shuang Ma
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Fishery Ecology Environment; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences.,College of Food Science and Technology, Shanghai Ocean University
| | - Lai Hao Li
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Fishery Ecology Environment; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
| | - Shu Xian Hao
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Fishery Ecology Environment; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
| | - Xian Qing Yang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Fishery Ecology Environment; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
| | - Hui Huang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Fishery Ecology Environment; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
| | - Jian Wei Cen
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Fishery Ecology Environment; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
| | - Yue Qi Wang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Fishery Ecology Environment; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
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18
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Fatemi N, Salehi N, Pignata L, Palumbo P, Cubellis MV, Ramazanali F, Ray P, Varkiani M, Reyhani-Sabet F, Biglari A, Sparago A, Acurzio B, Palumbo O, Carella M, Riccio A, Totonchi M. Biallelic variant in cyclin B3 is associated with failure of maternal meiosis II and recurrent digynic triploidy. J Med Genet 2020; 58:783-788. [PMID: 32938693 PMCID: PMC8551973 DOI: 10.1136/jmedgenet-2020-106909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/07/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022]
Abstract
Background Triploidy is one of the most common chromosome abnormalities affecting human gestation and accounts for an important fraction of first-trimester miscarriages. Triploidy has been demonstrated in a few cases of recurrent pregnancy loss (RPL) but its molecular mechanisms are unknown. This study aims to identify the genetic cause of RPL associated with fetus triploidy. Methods We investigated genomic imprinting, genotyped sequence-tagged site (STS) markers and performed exome sequencing in a family including two sisters with RPL. Moreover, we evaluated oocyte maturation in vivo and in vitro and effect of the candidate protein variant in silico. Results While features of hydatidiform mole were excluded, the presence of triploidy of maternal origin was demonstrated in the fetuses. Oocyte maturation was deficient and all the maternally inherited pericentromeric STS alleles were homozygous in the fetuses. A deleterious missense variant (p.V1251D) of the cyclin B3 gene (CCNB3) affecting a residue conserved in placental mammals and located in a region that can interact with the cyclin-dependent kinase 1 or cyclin-dependent kinase 2 cosegregated in homozygosity with RPL. Conclusion Here, we report a family in which a damaging variant in cyclin B3 is associated with the failure of oocyte meiosis II and recurrent fetus triploidy, implicating a rationale for CCNB3 testing in RPL.
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Affiliation(s)
- Nayeralsadat Fatemi
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran.,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Najmeh Salehi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Laura Pignata
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale delle Ricerche (CNR), Napoli, Italy
| | - Pietro Palumbo
- IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | | | - Fariba Ramazanali
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Pierre Ray
- Genetic Epigenetic and Therapies of Infertility, Institute for Advanced Biosciences, INSERM 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble F38000, France.,Unité Médicale de génétique de l'infertilité et de diagnostic pré-implantatoire (GI-DPI), Centre Hospitalier Universitaire Grenoble Alpes, Grenoble 38000, France
| | - Maryam Varkiani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Fakhreddin Reyhani-Sabet
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Alireza Biglari
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran
| | - Angela Sparago
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Basilia Acurzio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale delle Ricerche (CNR), Napoli, Italy
| | - Orazio Palumbo
- IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Massimo Carella
- IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Andrea Riccio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy .,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale delle Ricerche (CNR), Napoli, Italy
| | - Mehdi Totonchi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran .,Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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19
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Kottmann JS, Jørgensen MGP, Bertolini F, Loh A, Tomkiewicz J. Differential impacts of carp and salmon pituitary extracts on induced oogenesis, egg quality, molecular ontogeny and embryonic developmental competence in European eel. PLoS One 2020; 15:e0235617. [PMID: 32634160 PMCID: PMC7340298 DOI: 10.1371/journal.pone.0235617] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
Low egg quality and embryonic survival are critical challenges in aquaculture, where assisted reproduction procedures and other factors may impact egg quality. This includes European eel (Anguilla anguilla), where pituitary extract from carp (CPE) or salmon (SPE) is applied to override a dopaminergic inhibition of the neuroendocrine system, preventing gonadotropin secretion and gonadal development. The present study used either CPE or SPE to induce vitellogenesis in female European eel and compared impacts on egg quality and offspring developmental competence with emphasis on the maternal-to-zygotic transition (MZT). Females treated with SPE produced significantly higher proportions of floating eggs with fewer cleavage abnormalities and higher embryonic survival. These findings related successful embryogenesis to higher abundance of mRNA transcripts of genes involved in cell adhesion, activation of MZT, and immune response (dcbld1, epcam, oct4, igm) throughout embryonic development. The abundance of mRNA transcripts of cldnd, foxr1, cea, ccna1, ccnb1, ccnb2, zar1, oct4, and npm2 was relatively stable during the first eight hours, followed by a drop during MZT and low levels thereafter, indicating transfer and subsequent clearance of maternal mRNA. mRNA abundance of zar1, epcam, and dicer1 was associated with cleavage abnormalities, while mRNA abundance of zar1, sox2, foxr1, cldnd, phb2, neurod4, and neurog1 (before MZT) was associated with subsequent embryonic survival. In a second pattern, low initial mRNA abundance with an increase during MZT and higher levels persisting thereafter indicating the activation of zygotic transcription. mRNA abundance of ccna1, npm2, oct4, neurod4, and neurog1 during later embryonic development was associated with hatch success. A deviating pattern was observed for dcbld1, which mRNA levels followed the maternal-effect gene pattern but only for embryos from SPE treated females. Together, the differences in offspring production and performance reported in this study show that PE composition impacts egg quality and embryogenesis and in particular, the transition from initial maternal transcripts to zygotic transcription.
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Affiliation(s)
- Johanna S. Kottmann
- National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Francesca Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Adrian Loh
- School of Science, University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - Jonna Tomkiewicz
- National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
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20
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Domestication is associated with differential expression of pikeperch egg proteins involved in metabolism, immune response and protein folding. Animal 2020; 14:2336-2350. [PMID: 32525470 DOI: 10.1017/s1751731120001184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Domestication is a condition in which the breeding, care and feeding of animals are, at least in part, controlled by humans. Information regarding the changes in the protein composition of eggs in response to domestication is very limited. Such data are prerequisite for improvements in the reproduction of domesticated fish. The aim of this study was to examine the impact of domestication on the proteome of pikeperch eggs using two-dimensional differential in-gel electrophoresis. We analysed high-quality eggs from domesticated and wild pikeperch fish to reveal proteins that were presumably only related to the domestication process and not to the quality of eggs. Here, we show that domestication has a profound impact on the protein profile of pikeperch eggs. We identified 66 differentially abundant protein spots, including 27 spots that were more abundant in wild-caught pikeperch eggs and 39 spots that were enriched in eggs collected from domesticated females. Eggs originating from wild-caught females showed higher expression levels of proteins involved in folding, apoptotic process, purine metabolism and immune response, whereas eggs of domesticated females showed higher expression levels of proteins that participated mainly in metabolism. The changes in metabolic proteins in eggs from domesticated females can reflect the adaptation of pikeperch to commercial diets, which have profoundly distinct compositions compared with natural diets. The decrease in the abundance of proteins related to immune response in eggs from the domesticated population suggests that domestication may lead to disturbances in defence mechanisms. In turn, the lower abundance of heat shock proteins in eggs of domesticated fish may indicate their adaptation to stable farming conditions and reduced environmental stressors or their better tolerance of stress from breeding. The proteins identified in this study can increase our knowledge concerning the mechanism of the pikeperch domestication process.
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21
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Myers JN, Dyce PW, Chatakondi NG, Gorman SA, Quiniou SM, Su B, Peatman E, Dunham RA, Butts IA. Analysis of specific mRNA gene expression profiles as markers of egg and embryo quality for hybrid catfish aquaculture. Comp Biochem Physiol A Mol Integr Physiol 2020; 243:110675. [DOI: 10.1016/j.cbpa.2020.110675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023]
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Izumi H, Gen K, Lokman PM, Hagihara S, Horiuchi M, Tanaka T, Ijiri S, Adachi S. Maternal transcripts in good and poor quality eggs from Japanese eel,
Anguilla japonica
—their identification by large‐scale quantitative analysis. Mol Reprod Dev 2019; 86:1846-1864. [DOI: 10.1002/mrd.23273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/29/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Hikari Izumi
- Division of Marine Life ScienceHokkaido University Hokkaido Japan
| | - Koichiro Gen
- Seikai National Fisheries Research InstituteFisheries Research Agency Nagasaki Japan
| | - P. Mark Lokman
- Department of ZoologyUniversity of Otago Dunedin New Zealand
| | - Seishi Hagihara
- Division of Marine Life ScienceHokkaido University Hokkaido Japan
| | - Moemi Horiuchi
- Division of Marine Life ScienceHokkaido University Hokkaido Japan
| | - Toshiomi Tanaka
- Hamanako BranchShizuoka Prefectural Research Institute of Fishery Shizuoka Japan
| | - Shigeho Ijiri
- Division of Marine Life ScienceHokkaido University Hokkaido Japan
| | - Shinji Adachi
- Division of Marine Life ScienceHokkaido University Hokkaido Japan
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Mahanty A, Purohit GK, Mohanty S, Mohanty BP. Heat stress-induced alterations in the expression of genes associated with gonadal integrity of the teleost Puntius sophore. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:1409-1417. [PMID: 31144086 DOI: 10.1007/s10695-019-00643-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
Temperature plays an important role on reproductive physiology of vertebrates including mammals, fish, and birds. It has varying effects on fish reproduction depending on the species; higher temperatures favor the spring-spawning species, while lower temperatures stimulate reproduction in autumn spawners. To evaluate the impact of high temperature on the reproductive physiology of minnow Puntius sophore, we carried out expression analysis of selected genes associated with gamete quality (hsp60, hsp70, hsp90, hsf1, vtg), pleuripotency (sox2, oct4, nanog), and sex determination (dmrt1) in gonads (ovary and testis) of P. sophore, heat stressed for different time periods (36 °C/7 days or 60 days) using real-time quantitative polymerase chain reaction (RT-qPCR). Expression of most of the hsp, vtg, and pleuripotency marker genes sox-2, oct-4, and nanog genes was downregulated in both ovary and testis of heat-stressed fish. The expression of dmrt-1 was upregulated in testis but downregulated in ovary of the heat-stressed fish which could be a male favoring effect of high temperature in P. sophore. This study suggests that the reproductive physiology and health of the nutrient dense P. sophore would be negatively affected by high temperature stress.
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Affiliation(s)
- Arabinda Mahanty
- Fishery Resource and Environmental Management Division, Biochemistry Laboratory, ICAR - Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, 753 006, India
| | - Gopal Krishna Purohit
- School of Biotechnology, KIIT Deemed University, Bhubaneswar, 751024, India
- Santaan Fertility Centre and Research Institute, KIIT-TBI, KIIT Deemed University, Bhubaneswar, 751024, India
| | - Sasmita Mohanty
- School of Biotechnology, KIIT Deemed University, Bhubaneswar, 751024, India.
- Department of Biotechnology, Ramadevi Women's University, Bhubaneswar, India.
| | - Bimal Prasanna Mohanty
- Fishery Resource and Environmental Management Division, Biochemistry Laboratory, ICAR - Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India.
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Tang L, Chen J, Ye Z, Zhao M, Meng Z, Lin H, Li S, Zhang Y. Transcriptomic Analysis Revealed the Regulatory Mechanisms of Oocyte Maturation and Hydration in Orange-Spotted Grouper (Epinephelus coioides). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:537-549. [PMID: 31129797 DOI: 10.1007/s10126-019-09902-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Oocyte maturation and hydration are regulated by a complex interplay of various hormones and local factors. We have investigated the morphological changes of follicles and serum steroid levels during the HCG (human choionic gonadotophin)-induced oocyte maturation in the orange-spotted grouper. For the first time, a large-scale transcriptomic analysis of follicles during the maturation has been conducted in a fish species which produce pelagic oocytes. Eight cDNA libraries of follicle samples, from full-grown immature follicles to mature follicles, were constructed. A total of 402,530,284 high-quality clean reads were obtained after filtering, 79.66% of which perfectly mapped to the orange-spotted grouper genome. Real-time PCR results of 12 representative genes related to oocyte maturation and hydration verified the reliability of the RNA-seq data. A large number of genes related to oocyte maturation and hydration were identified in the transcriptome dataset. And the transcriptomic analysis revealed the dynamic changes of the steroid synthesis pathway and the pathway of hydration during oocyte maturation. The present study will facilitate future study on the oocyte maturation and hydration in the orange-spotted grouper and other marine pelagic egg spawner.
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Affiliation(s)
- Lin Tang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jiaxing Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhifeng Ye
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Mi Zhao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Guangdong Ocean University, Zhanjiang, 524088, China.
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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25
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Ma H, Martin K, Dixon D, Hernandez AG, Weber GM. Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss. BMC Genomics 2019; 20:319. [PMID: 31029084 PMCID: PMC6486991 DOI: 10.1186/s12864-019-5690-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/11/2019] [Indexed: 12/31/2022] Open
Abstract
Background Maternal transcripts are accumulated in the oocyte during oogenesis to provide for protein synthesis from oocyte maturation through early embryonic development, when nuclear transcription is silenced. The maternal mRNAs have short poly(A) tails after undergoing post-transcriptional processing necessary for stabilizing them for storage. The transcripts undergo cytoplasmic polyadenylation when they are to be translated. Transcriptome analyses comparing total mRNA and elongated poly(A) mRNA content among eggs of different quality can provide insight into molecular mechanisms affecting egg developmental competence in rainbow trout. The present study used RNA-seq to compare transcriptomes of unfertilized eggs of rainbow trout females yielding different eyeing rates, following rRNA removal and poly(A) retention for construction of the libraries. Results The percentage of embryos to reach the 32-cell stage at 24 h post fertilization was significantly correlated to family eyeing rate, indicating that inviable embryos were developmentally compromised before zygotic genome activation. RNA sequencing identified 2 differentially expressed transcripts (DETs) from total mRNA sequencing comparing females with low-quality (< 5% eyeing), medium-quality (30–50% eyeing), and high-quality (> 80% eyeing) eggs. In contrast, RNA sequencing from poly(A) captured transcripts identified 945 DETs between low- and high-quality eggs, 1012 between low- and medium-quality eggs, and only 2 between medium- and high-quality eggs. The transcripts of mitochondrial genes were enriched with polyadenylated transcript sequencing and they were significantly reduced in low-quality eggs. Similarly, mitochondrial DNA was reduced in low-quality eggs compared with medium- and high-quality eggs. The functional gene analysis classified the 945 DETs between low- and high-quality eggs into 31 functional modules, many of which were related to ribosomal and mitochondrial functions. Other modules involved transcription, translation, cell division, apoptosis, and immune responses. Conclusions Our results indicate that differences in egg quality may be derived from differences in maternal nuclear transcript activation and cytoplasmic polyadenylation before ovulation, as opposed to accumulation and storage of maternal nuclear transcripts during oogenesis. Transcriptome comparisons suggest low-quality eggs suffered from impaired oxidative phosphorylation and translation. The DETs identified in this study provide insight into developmental competence in rainbow trout eggs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5690-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Ma
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | | | | | | | - Gregory M Weber
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA.
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26
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Wang Y, Zhang M, Qin Q, Peng Y, Huang X, Wang C, Cao L, Li W, Tao M, Zhang C, Liu S. Transcriptome Profile Analysis on Ovarian Tissues of Autotetraploid Fish and Diploid Red Crucian Carp. Front Genet 2019; 10:208. [PMID: 30941161 PMCID: PMC6434244 DOI: 10.3389/fgene.2019.00208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/26/2019] [Indexed: 12/27/2022] Open
Abstract
Polyploidization can significantly alter the size of animal gametes. Autotetraploid fish (RRRR, 4nRR = 200) (4nRR) possessing four sets of chromosomes were derived from whole-genome duplication in red crucian carp (RR, 2n = 100) (RCC). The diploid eggs of the 4nRR fish were significantly larger than the eggs of RCC. To explore the differences between the ovaries of these two ploidies of fishes at the molecular level, we compared the ovary transcriptome profiles of 4nRR fish and RCC and identified differentially expressed genes (DEGs). A total of 19,015 unigenes were differentially expressed between 4nRR fish and RCC, including 12,591 upregulated and 6,424 downregulated unigenes in 4nRR fish. Functional analyses revealed that eight genes (CDKL1, AHCY, ARHGEF3, TGFβ, WNT11, CYP27A, GDF7, and CKB) were involved in the regulation of cell proliferation, cell division, gene transcription, ovary development and energy metabolism, suggesting that these eight genes were related to egg size in 4nRR fish and RCC. We validated the expression levels of these eight DEGs in 4nRR fish and RCC using quantitative PCR. The study results provided insights into the regulatory mechanisms underlying the differences in crucian carp egg sizes.
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Affiliation(s)
- Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Minghe Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yajun Peng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Liu Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Wuhui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
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27
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Oogenesis and Egg Quality in Finfish: Yolk Formation and Other Factors Influencing Female Fertility. FISHES 2018. [DOI: 10.3390/fishes3040045] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Egg quality in fishes has been a topic of research in aquaculture and fisheries for decades as it represents an important life history trait and is critical for captive propagation and successful recruitment. A major factor influencing egg quality is proper yolk formation, as most fishes are oviparous and the developing offspring are entirely dependent on stored egg yolk for nutritional sustenance. These maternally derived nutrients consist of proteins, carbohydrates, lipids, vitamins, minerals, and ions that are transported from the liver to the ovary by lipoprotein particles including vitellogenins. The yolk composition may be influenced by broodstock diet, husbandry, and other intrinsic and extrinsic conditions. In addition, a number of other maternal factors that may influence egg quality also are stored in eggs, such as gene transcripts, that direct early embryonic development. Dysfunctional regulation of gene or protein expression may lead to poor quality eggs and failure to thrive within hours of fertilization. These gene transcripts may provide important markers as their expression levels may be used to screen broodstock for potential spawning success. In addition to such intrinsic factors, stress may lead to ovarian atresia or reproductive failure and can impact fish behavior, fecundity, and ovulation rate. Finally, postovulatory aging may occur when eggs become overripe and the fish fails to spawn in a timely fashion, leading to low fertility, often encountered during manual strip spawning of fish.
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28
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Sarropoulou E, Sundaram AYM, Kaitetzidou E, Kotoulas G, Gilfillan GD, Papandroulakis N, Mylonas CC, Magoulas A. Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili. Gigascience 2018; 6:1-13. [PMID: 29126158 PMCID: PMC5751066 DOI: 10.1093/gigascience/gix108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/02/2017] [Indexed: 02/05/2023] Open
Abstract
Background Teleosts of the genus Seriola, commonly known as amberjacks, are of high commercial value in international markets due to their flesh quality and worldwide distribution. The Seriola species of interest to Mediterranean aquaculture is the greater amberjack (Seriola dumerili). This species holds great potential for the aquaculture industry, but in captivity, reproduction has proved to be challenging, and observed growth dysfunction hinders their domestication. Insights into molecular mechanisms may contribute to a better understanding of traits like growth and sex, but investigations to unravel the molecular background of amberjacks have begun only recently. Findings Illumina HiSeq sequencing generated a high-coverage greater amberjack genome sequence comprising 45 909 scaffolds. Comparative mapping to the Japanese yellowtail (Seriola quinqueriadiata) and to the model species medaka (Oryzias latipes) allowed the generation of in silico groups. Additional gonad transcriptome sequencing identified sex-biased transcripts, including known sex-determining and differentiation genes. Investigation of the muscle transcriptome of slow-growing individuals showed that transcripts involved in oxygen and gas transport were differentially expressed compared with fast/normal-growing individuals. On the other hand, transcripts involved in muscle functions were found to be enriched in fast/normal-growing individuals. Conclusion The present study provides the first insights into the molecular background of male and female amberjacks and of fast- and slow-growing fish. Therefore, valuable molecular resources have been generated in the form of a first draft genome and a reference transcriptome. Sex-biased genes, which may also have roles in sex determination or differentiation, and genes that may be responsible for slow growth are suggested.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
| | - Arvind Y M Sundaram
- Norwegian High Throughput Sequencing Centre, Department of Medical Genetics, Oslo University Hospital (Ullevål), Kirkeveien 166 0450, Oslo, Norway
| | - Elisavet Kaitetzidou
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
| | - Gregor D Gilfillan
- Norwegian High Throughput Sequencing Centre, Department of Medical Genetics, Oslo University Hospital (Ullevål), Kirkeveien 166 0450, Oslo, Norway
| | - Nikos Papandroulakis
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
| | - Constantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
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Youneszadeh-Fashalami M, Salati AP, Keyvanshokooh S. Comparison of proteomic profiles in the ovary of Sterlet sturgeon (Acipenser ruthenus) during vitellogenic stages. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 27:23-29. [PMID: 29738886 DOI: 10.1016/j.cbd.2018.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 11/29/2022]
Abstract
One of the challenges of sturgeon aquaculture is that sturgeon takes an extended amount of time to reach sexual maturity. The pattern of the protein expression in relation to the late maturity of sturgeon can help to better understand changes in sexual maturity. 17β-estradiol (E2), testosterone (T) and vitellogenin (Vtg) levels were examined at all stages of sexual maturation in Sterlet sturgeon (Acipenser ruthenus). Two-dimensional gel electrophoresis and mass spectrometry analysis were used to show the pattern of the ovarian proteins. The T levels increased from the previtellogenic to the postvitellogenic stages (P < 0.05) and Vtg showed a decremental pattern in pre- and postvitellogenic, and atresia (not significantly). The analysis showed 900 protein spots, 19 of which were successfully identified and had significant differences between the previtellogenic and the vitellogenic groups (P < 0.05). Among the identified proteins, 40% involved in cell defense (heat shock protein, Glutathione peroxidase, natural killer enhancing factor, peroxiredoxin-2), 30% in transcription and translation (constitutive photomorphogenesis 9 and Ybx2), 20% in metabolism and energy production (triose-phosphate isomerase (TPI)) and 10% in transport (glycolipid transfer protein). In the vitellogenic stage, the proteins were related to metabolism and energy production (TPI, ES1, creatin kinase, enolase, nucleoside diphosphate kinase, 50%), cell defense (thioredoxin and dislophid isomerase, 20%) and transport (fatty acid binding protein, 10%). Our findings show changes in protein expression pattern from cell defense to metabolism during egg development.
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Affiliation(s)
- Mohammad Youneszadeh-Fashalami
- Department of Fisheries, Faculty of marine Natural Resources, Khorramshahr University of Marine Science and Technology, Iran; South Iranian Aquaculture Research Center, Ahwaz, Iran
| | - Amir Parviz Salati
- Department of Fisheries, Faculty of marine Natural Resources, Khorramshahr University of Marine Science and Technology, Iran.
| | - Saeed Keyvanshokooh
- Department of Fisheries, Faculty of marine Natural Resources, Khorramshahr University of Marine Science and Technology, Iran
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Woods LC, Li Y, Ding Y, Liu J, Reading BJ, Fuller SA, Song J. DNA methylation profiles correlated to striped bass sperm fertility. BMC Genomics 2018; 19:244. [PMID: 29636007 PMCID: PMC5894188 DOI: 10.1186/s12864-018-4548-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 02/13/2018] [Indexed: 01/11/2023] Open
Abstract
Background Striped bass (Morone saxatilis) spermatozoa are used to fertilize in vitro the eggs of white bass (M. chrysops) to produce the preferred hybrid for the striped bass aquaculture industry. Currently, only one source of domestic striped bass juveniles is available to growers that is not obtained from wild-caught parents and is thus devoid of any genetic improvement in phenotypic traits of importance to aquaculture. Sperm epigenetic modification has been predicted to be associated with fertility, which could switch genes on and off without changing the DNA sequence itself. DNA methylation is one of the most common epigenetic modification types and changes in sperm epigenetics can be correlated to sub-fertility or infertility in male striped bass. The objective of this study was to find the differentially methylated regions (DMRs) between high-fertility and sub-fertility male striped bass, which could potentially regulate the fertility performance. Results In our present study, we performed DNA methylation analysis of high-fertility and sub-fertility striped bass spermatozoa through MBD-Seq methods. A total of 171 DMRs were discovered in striped bass sperm correlated to fertility. Based on the annotation of these DMRs, we conducted a functional classification analysis and two important groups of genes including the WDR3/UTP12 and GPCR families, were discovered to be related to fertility performance of striped bass. Proteins from the WDR3/UTP12 family are involved in forming the sperm flagella apparatus in vertebrates and GPCRs are involved in hormonal signaling and regulation of tissue development, proliferation and differentiation. Conclusions Our results contribute insights into understanding the mechanism of fertility in striped bass, which will provide powerful tools to maximize reproductive efficiencies and to identify those males with superior gametes for this important aquaculture species. Electronic supplementary material The online version of this article (10.1186/s12864-018-4548-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- L Curry Woods
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou, GD, 510642, China.
| | - Yi Ding
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Jianan Liu
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Benjamin J Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695, USA
| | - S Adam Fuller
- HKD Stuttgart National Aquaculture Research Center, Agricultural Research Service, US Department of Agriculture, Stuttgart, AR, 72160, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
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31
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Adrian-Kalchhauser I, Walser JC, Schwaiger M, Burkhardt-Holm P. RNA sequencing of early round goby embryos reveals that maternal experiences can shape the maternal RNA contribution in a wild vertebrate. BMC Evol Biol 2018; 18:34. [PMID: 29566669 PMCID: PMC5863367 DOI: 10.1186/s12862-018-1132-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/29/2018] [Indexed: 01/01/2023] Open
Abstract
Background It has been proposed that non-genetic inheritance could promote species fitness. Non-genetic inheritance could allow offspring to benefit from the experience of their parents, and could advocate pre-adaptation to prevailing and potentially selective conditions. Indeed, adaptive parental effects have been modeled and observed, but the molecular mechanisms behind them are far from understood. Results In the present study, we investigated whether maternal RNA can carry information about environmental conditions experienced by the mother in a wild vertebrate. Maternal RNA directs the development of the early embryo in many non-mammalian vertebrates and invertebrates. However, it is not known whether vertebrate maternal RNA integrates information about the parental environment. We sequenced the maternal RNA contribution from a model that we expected to rely on parental effects: the invasive benthic fish species Neogobius melanostomus (Round Goby). We found that maternal RNA expression levels correlated with the water temperature experienced by the mother before oviposition, and identified temperature-responsive gene groups such as core nucleosome components or the microtubule cytoskeleton. Conclusions Our findings suggest that the maternal RNA contribution may incorporate environmental information. Maternal RNA should therefore be considered a potentially relevant pathway for non-genetic inheritance. Also, the ability of a species to integrate environmental information in the maternal RNA contribution could potentially contribute to species fitness and may also play a role in extraordinary adaptive success stories of invasive species such as the round goby. Electronic supplementary material The online version of this article (10.1186/s12862-018-1132-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
| | - Jean-Claude Walser
- Department of Environmental Systems Science, Genetic Diversity Centre Zurich, ETH Zurich, Universitätstrasse 16, CH-8092, Zurich, Switzerland
| | - Michaela Schwaiger
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Patricia Burkhardt-Holm
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
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Douros JD, Baltzegar DA, Reading BJ, Seale AP, Lerner DT, Grau EG, Borski RJ. Leptin Stimulates Cellular Glycolysis Through a STAT3 Dependent Mechanism in Tilapia. Front Endocrinol (Lausanne) 2018; 9:465. [PMID: 30186233 PMCID: PMC6110908 DOI: 10.3389/fendo.2018.00465] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/27/2018] [Indexed: 12/18/2022] Open
Abstract
We assessed if leptin, a cytokine hormone known to enhance energy expenditure by promoting lipid and carbohydrate catabolism in response to physiologic stress, might directly regulate cellular glycolysis. A transcriptomic analysis of prolactin cells in the tilapia (Oreochromis mossambicus) pituitary rostral pars distalis (RPD) revealed that recombinant leptin (rtLep) differentially regulates 1,995 genes, in vitro. Machine learning algorithms and clustering analyses show leptin influences numerous cellular gene networks including metabolism; protein processing, transport, and metabolism; cell cycle and the hypoxia response. Leptin stimulates transcript abundance of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (gapdh) in a covariate manner to the hypoxic stress gene network. Orthogonal tests confirm that rtLepA dose-dependently increases gapdh gene expression in the RPD along with transcript abundance of 6-phosphofructo-1-kinase (pfk1), the rate limiting glycolytic enzyme. Functional testing demonstrated that leptin stimulates PFK activity and glycolytic output, while Stattic (a STAT3 blocker) was sufficient to suppress these responses, indicating leptin stimulates glycolysis through a STAT3-dependent mechanism. Leptin also stimulated pfk1 gene expression and lactate production in primary hepatocyte incubations in a similar manner to those shown for the pituitary RPD. This work characterizes a critical metabolic action of leptin to directly stimulate glycolysis across tissue types in a teleost model system, and suggest that leptin may promote energy expenditure, in part, by stimulating glycolysis. These data in a teleost fish, suggest that one of leptin's ancient, highly-conserved functions among vertebrates may be stimulation of glycolysis to facilitate the energetic needs associated with various stressors.
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Affiliation(s)
- Jonathan D. Douros
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - David A. Baltzegar
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- Genomics Sciences Laboratory, North Carolina State University, Raleigh, NC, United States
| | - Benjamin J. Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Andre P. Seale
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, United States
- Department of Human Nutrition, Food, and Animal Sciences, University of Hawaii at Mānoa, Honolulu, HI, United States
| | - Darren T. Lerner
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, United States
- University of Hawaii Sea Grant College Program, Honolulu, HI, United States
| | - E. Gordon Grau
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, United States
| | - Russell J. Borski
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Russell J. Borski
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Comparative transcriptome analysis of ovary and testis reveals potential sex-related genes and pathways in spotted knifejaw Oplegnathus punctatus. Gene 2017; 637:203-210. [DOI: 10.1016/j.gene.2017.09.055] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/12/2017] [Accepted: 09/25/2017] [Indexed: 12/22/2022]
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Yilmaz O, Patinote A, Nguyen TV, Com E, Lavigne R, Pineau C, Sullivan CV, Bobe J. Scrambled eggs: Proteomic portraits and novel biomarkers of egg quality in zebrafish (Danio rerio). PLoS One 2017; 12:e0188084. [PMID: 29145436 PMCID: PMC5690628 DOI: 10.1371/journal.pone.0188084] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 10/31/2017] [Indexed: 01/08/2023] Open
Abstract
Egg quality is a complex biological trait and a major determinant of reproductive fitness in all animals. This study delivered the first proteomic portraits of egg quality in zebrafish, a leading biomedical model for early development. Egg batches of good and poor quality, evidenced by embryo survival for 24 h, were sampled immediately after spawning and used to create pooled or replicated sample sets whose protein extracts were subjected to different levels of fractionation before liquid chromatography and tandem mass spectrometry. Obtained spectra were searched against a zebrafish proteome database and detected proteins were annotated, categorized and quantified based on normalized spectral counts. Manually curated and automated enrichment analyses revealed poor quality eggs to be deficient of proteins involved in protein synthesis and energy and lipid metabolism, and of some vitellogenin products and lectins, and to have a surfeit of proteins involved in endo-lysosomal activities, autophagy, and apoptosis, and of some oncogene products, lectins and egg envelope proteins. Results of pathway and network analyses suggest that this aberrant proteomic profile results from failure of oocytes giving rise to poor quality eggs to properly transit through final maturation, and implicated Wnt signaling in the etiology of this defect. Quantitative comparisons of abundant proteins in good versus poor quality eggs revealed 17 candidate egg quality markers. Thus, the zebrafish egg proteome is clearly linked to embryo developmental potential, a phenomenon that begs further investigation to elucidate the root causes of poor egg quality, presently a serious and intractable problem in livestock and human reproductive medicine.
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Affiliation(s)
- Ozlem Yilmaz
- Laboratory of Fish Physiology and Genomics, INRA UR1037, Rennes Cedex, France
| | - Amélie Patinote
- Laboratory of Fish Physiology and Genomics, INRA UR1037, Rennes Cedex, France
| | - Thao Vi Nguyen
- Laboratory of Fish Physiology and Genomics, INRA UR1037, Rennes Cedex, France
| | | | | | | | | | - Julien Bobe
- Laboratory of Fish Physiology and Genomics, INRA UR1037, Rennes Cedex, France
- * E-mail:
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Liu DT, Brewer MS, Chen S, Hong W, Zhu Y. Transcriptomic signatures for ovulation in vertebrates. Gen Comp Endocrinol 2017; 247:74-86. [PMID: 28111234 PMCID: PMC5410184 DOI: 10.1016/j.ygcen.2017.01.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/14/2017] [Accepted: 01/17/2017] [Indexed: 01/01/2023]
Abstract
The central roles of luteinizing hormone (LH), progestin and their receptors for initiating ovulation have been well established. However, signaling pathways and downstream targets such as proteases that are essential for the rupture of follicular cells are still unclear. Recently, we found anovulation in nuclear progestin receptor (Pgr) knockout (Pgr-KO) zebrafish, which offers a new model for examining genes and pathways that are important for ovulation and fertility. In this study, we examined expression of all transcripts using RNA-Seq in preovulatory follicular cells collected following the final oocyte maturation, but prior to ovulation, from wild-type (WT) or Pgr-KO fish. Differential expression analysis revealed 3567 genes significantly differentially expressed between WT and Pgr-KO fish (fold change⩾2, p<0.05). Among those, 1543 gene transcripts were significantly more expressed, while 2024 genes were significantly less expressed, in WT than those in Pgr-KO. We then retrieved and compared transcriptional data from online databases and further identified 661 conserved genes in fish, mice, and humans that showed similar levels of high (283 genes) or low (387) expression in animals that were ovulating compared to those with no ovulation. For the first time, ovulatory genes and their involved biological processes and pathways were also visualized using Enrichment Map and Cytoscape. Intriguingly, enrichment analysis indicated that the genes with higher expression were involved in multiple ovulatory pathways and processes such as inflammatory response, angiogenesis, cytokine production, cell migration, chemotaxis, MAPK, focal adhesion, and cytoskeleton reorganization. In contrast, the genes with lower expression were mainly involved in DNA replication, DNA repair, DNA methylation, RNA processing, telomere maintenance, spindle assembling, nuclear acid transport, catabolic processes, and nuclear and cell division. Our results indicate that a large set of genes (>3000) is differentially regulated in the follicular cells in zebrafish prior to ovulation, terminating programs such as growth and proliferation, and beginning processes including the inflammatory response and apoptosis. Further studies are required to establish relationships among these genes and an ovulatory circuit in the zebrafish model.
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Affiliation(s)
- Dong Teng Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian Province 361102, People's Republic of China; Department of Biology, East Carolina University, Greenville, NC 27858, United States
| | - Michael S Brewer
- Department of Biology, East Carolina University, Greenville, NC 27858, United States
| | - Shixi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian Province 361102, People's Republic of China
| | - Wanshu Hong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian Province 361102, People's Republic of China
| | - Yong Zhu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian Province 361102, People's Republic of China; Department of Biology, East Carolina University, Greenville, NC 27858, United States.
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Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Khalil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, Zhou T. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 2017; 18:191. [PMID: 28219347 PMCID: PMC5319170 DOI: 10.1186/s12864-017-3557-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
Abstract
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.
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Affiliation(s)
- Hisham Abdelrahman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mohamed ElHady
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Standish Allen
- Aquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Rafet Al-Tobasei
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Lisui Bao
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ben Beck
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Harvey Blackburn
- USDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO, 80521-4500, USA
| | - Brian Bosworth
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - John Buchanan
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA, 92121, USA
| | - Jesse Chappell
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - William Daniels
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sheng Dong
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Evan Durland
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Kamal Gosh
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Perry Hackett
- Department of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN, 55455, USA
| | - Terry Hanson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dennis Hedgecock
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Tiffany Howard
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Leigh Holland
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Molly Jackson
- Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA, 98584, USA
| | - Yulin Jin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Karim Khalil
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Thomas Kocher
- Department of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD, 20742, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Ning Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lauren Lindsey
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Kyle Martin
- Troutlodge, 27090 Us Highway 12, Naches, WA, 98937, USA
| | - Romi Novriadi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ramjie Odin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dina Proestou
- USDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Guyu Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Benjamin Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695-7617, USA
| | - Caird Rexroad
- USDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD, 20705, USA
| | - Steven Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Mohamed Salem
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Andrew Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA
| | - Huitong Shi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Craig Shoemaker
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sheila Stiles
- USDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut, 06460, USA
| | - Suxu Tan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Kathy F J Tang
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Terrence Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70820, USA
| | - Joseph Tomasso
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wendy Tri Prabowo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | | | - Khoi Vo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Geoff Waldbieser
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - Hanping Wang
- Aquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH, 45661, USA
| | - Xiaozhu Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yujia Yang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Yant
- Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS, 38753, USA
| | - Zihao Yuan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
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Salger SA, Reading BJ, Noga EJ. Tissue localization of piscidin host-defense peptides during striped bass (Morone saxatilis) development. FISH & SHELLFISH IMMUNOLOGY 2017; 61:173-180. [PMID: 28034834 DOI: 10.1016/j.fsi.2016.12.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 12/07/2016] [Accepted: 12/23/2016] [Indexed: 06/06/2023]
Abstract
Infectious diseases are a major cause of larval mortality in finfish aquaculture. Understanding ontogeny of the fish immune system and thus developmental timing of protective immune tissues and cells, may help to decrease serious losses of larval fishes when they are particularly vulnerable to infection. One component of the innate immune system of fishes is the host-defense peptides, which include the piscidins. Piscidins are small, amphipathic, α-helical peptides with a broad-spectrum of action against viral, bacterial, fungal, and protozoan pathogens. We describe for the first time the cellular and tissue localization of three different piscidins (1, 3, and 4) during striped bass (Morone saxatilis) larval ontogeny using immunofluorescent histochemistry. From 16 days post hatch to 12 months of age, piscidin staining was observed in cells of the epithelial tissues of gill, digestive tract, and skin, mainly in mast cells. Staining was also seen in presumptive hematopoietic cells in the head kidney. The three piscidins showed variable cellular and tissue staining patterns, possibly relating to differences in tissue susceptibility or pathogen specificity. This furthers our observation that the piscidins are not a monolithic family of antimicrobials, but that different AMPs have different (more specialized) functions. Furthermore, no immunofluorescent staining of piscidins was observed in post-vitellogenic oocytes, embryos, or larvae from hatch to 14 days post hatch, indicating that this critical component of the innate immune system is inactive in pre-hatch and young larval striped bass.
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Affiliation(s)
- Scott A Salger
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States.
| | - Benjamin J Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Edward J Noga
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, United States
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Żarski D, Nguyen T, Le Cam A, Montfort J, Dutto G, Vidal MO, Fauvel C, Bobe J. Transcriptomic Profiling of Egg Quality in Sea Bass (Dicentrarchus labrax) Sheds Light on Genes Involved in Ubiquitination and Translation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:102-115. [PMID: 28181038 PMCID: PMC5323488 DOI: 10.1007/s10126-017-9732-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/09/2017] [Indexed: 05/31/2023]
Abstract
Variable and low egg quality is a major limiting factor for the development of efficient aquaculture production. This stems from limited knowledge on the mechanisms underlying egg quality in cultured fish. Molecular analyses, such as transcriptomic studies, are valuable tools to identify the most important processes modulating egg quality. However, very few studies have been devoted to this aspect so far. Within this study, the microarray-based transcriptomic analysis of eggs (of different quality) of sea bass (Dicentrarchus labrax) was performed. An Agilent oligo microarray experiment was performed on labelled mRNA extracted from 16 batches of eggs (each batch obtained from a different female) of sea bass, in which over 24,000 published probe arrays were used. We identified 39 differentially expressed genes exhibiting a differential expression between the groups of low (fertilization rate < 60 %) and high (fertilization rate > 60 %) quality. The mRNA levels of eight genes were further analyzed by quantitative PCR. Seven genes were confirmed by qPCR to be differentially expressed in eggs of low and high quality. This study confirmed the importance of some of the genes already reported to be potential molecular quality indicators (mainly rnf213 and irf7), but we also found new genes (mainly usp5, mem-prot, plec, cenpf), which had not yet been reported to be quality-dependent in fish. These results suggest the importance of genes involved in several important processes, such as protein ubiquitination, translation, DNA repair, and cell structure and architecture; these probably being the mechanisms that contribute to egg developmental competence in sea bass.
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Affiliation(s)
- Daniel Żarski
- Department of Lake and River Fisheries, University of Warmia and Mazury, ul. Oczapowskiego 2, 10-719, Olsztyn, Poland.
- Department of Aquaculture, Szent István University, Páter Károly 1, Gödöllo, 2100, Hungary.
| | | | | | | | - Gilbert Dutto
- IFREMER, UMR MARBEC (IRD, IFREMER, CNRS, Université de Montpellier), Station Expérimentale d'Aquaculture, Chemin de Maguelone, 34250, Palavas, France
| | - Marie Odile Vidal
- IFREMER, UMR MARBEC (IRD, IFREMER, CNRS, Université de Montpellier), Station Expérimentale d'Aquaculture, Chemin de Maguelone, 34250, Palavas, France
| | - Christian Fauvel
- IFREMER, UMR MARBEC (IRD, IFREMER, CNRS, Université de Montpellier), Station Expérimentale d'Aquaculture, Chemin de Maguelone, 34250, Palavas, France
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Luo H, Xiao S, Ye H, Zhang Z, Lv C, Zheng S, Wang Z, Wang X. Identification of Immune-Related Genes and Development of SSR/SNP Markers from the Spleen Transcriptome of Schizothorax prenanti. PLoS One 2016; 11:e0152572. [PMID: 27019203 PMCID: PMC4809619 DOI: 10.1371/journal.pone.0152572] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/16/2016] [Indexed: 12/21/2022] Open
Abstract
Schizothorax prenanti (S. prenanti) is mainly distributed in the upstream regions of the Yangtze River and its tributaries in China. This species is indigenous and commercially important. However, in recent years, wild populations and aquacultures have faced the serious challenges of germplasm variation loss and an increased susceptibility to a range of pathogens. Currently, the genetics and immune mechanisms of S. prenanti are unknown, partly due to a lack of genome and transcriptome information. Here, we sought to identify genes related to immune functions and to identify molecular markers to study the function of these genes and for trait mapping. To this end, the transcriptome from spleen tissues of S. prenanti was analyzed and sequenced. Using paired-end reads from the Illumina Hiseq2500 platform, 48,517 transcripts were isolated from the spleen transcriptome. These transcripts could be clustered into 37,785 unigenes with an N50 length of 2,539 bp. The majority of the unigenes (35,653, 94.4%) were successfully annotated using non-redundant nucleotide sequence analysis (nt), and the non-redundant protein (nr), Swiss-Prot, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. KEGG pathway assignment identified more than 500 immune-related genes. Furthermore, 7,545 putative simple sequence repeats (SSRs), 857,535 single nucleotide polymorphisms (SNPs), and 53,481 insertion/deletion (InDels) were detected from the transcriptome. This is the first reported high-throughput transcriptome analysis of S. prenanti, and it provides valuable genetic resources for the investigation of immune mechanisms, conservation of germplasm, and molecular marker-assisted breeding of S. prenanti.
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Affiliation(s)
- Hui Luo
- College of Animal Science & Technology, Hunan Agricultural University, Changsha, Hunan, China
- Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, Hunan, China
| | - Shijun Xiao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Hua Ye
- Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China
| | - Zhengshi Zhang
- Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China
| | - Changhuan Lv
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Shuming Zheng
- Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Xiaoqing Wang
- College of Animal Science & Technology, Hunan Agricultural University, Changsha, Hunan, China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, Hunan, China
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40
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Kohn YY, Symonds JE, Kleffmann T, Nakagawa S, Lagisz M, Lokman PM. Proteomic analysis of early-stage embryos: implications for egg quality in hapuku (Polyprion oxygeneios). FISH PHYSIOLOGY AND BIOCHEMISTRY 2015; 41:1403-1417. [PMID: 26183261 DOI: 10.1007/s10695-015-0095-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 07/06/2015] [Indexed: 06/04/2023]
Abstract
In order to develop biomarkers that may help predict the egg quality of captive hapuku (Polyprion oxygeneios) and provide potential avenues for its manipulation, the present study (1) sequenced the proteome of early-stage embryos using isobaric tag for relative and absolute quantification analysis, and (2) aimed to establish the predictive value of the abundance of identified proteins with regard to egg quality through regression analysis. Egg quality was determined for eight different egg batches by blastomere symmetry scores. In total, 121 proteins were identified and assigned to one of nine major groups according to their function/pathway. A mixed-effects model analysis revealed a decrease in relative protein abundance that correlated with (decreasing) egg quality in one major group (heat-shock proteins). No differences were found in the other protein groups. Linear regression analysis, performed for each identified protein separately, revealed seven proteins that showed a significant decrease in relative abundance with reduced blastomere symmetry: two correlates that have been named in other studies (vitellogenin, heat-shock protein-70) and a further five new candidate proteins (78 kDa glucose-regulated protein, elongation factor-2, GTP-binding nuclear protein Ran, iduronate 2-sulfatase and 6-phosphogluconate dehydrogenase). Notwithstanding issues associated with multiple statistical testing, we conclude that these proteins, and especially iduronate 2-sulfatase and the generic heat-shock protein group, could serve as biomarkers of egg quality in hapuku.
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Affiliation(s)
- Yair Y Kohn
- Department of Zoology, University of Otago, PO Box 56, 340 Great King St., Dunedin, 9016, New Zealand
- Bream Bay Aquaculture Park, NIWA, PO Box 147, Ruakaka, 0151, New Zealand
- Arava Research and Development Station, Hatzeva, Israel
| | - Jane E Symonds
- Bream Bay Aquaculture Park, NIWA, PO Box 147, Ruakaka, 0151, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Malgorzata Lagisz
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - P Mark Lokman
- Department of Zoology, University of Otago, PO Box 56, 340 Great King St., Dunedin, 9016, New Zealand.
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41
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Sullivan CV, Chapman RW, Reading BJ, Anderson PE. Transcriptomics of mRNA and egg quality in farmed fish: Some recent developments and future directions. Gen Comp Endocrinol 2015; 221:23-30. [PMID: 25725305 DOI: 10.1016/j.ygcen.2015.02.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 02/14/2015] [Accepted: 02/18/2015] [Indexed: 11/29/2022]
Abstract
Maternal mRNA transcripts deposited in growing oocytes regulate early development and are under intensive investigation as determinants of egg quality. The research has evolved from single gene studies to microarray and now RNA-Seq analyses in which mRNA expression by virtually every gene can be assessed and related to gamete quality. Such studies have mainly focused on genes changing two- to several-fold in expression between biological states, and have identified scores of candidate genes and a few gene networks whose functioning is related to successful development. However, ever-increasing yields of information from high throughput methods for detecting transcript abundance have far outpaced progress in methods for analyzing the massive quantities of gene expression data, and especially for meaningful relation of whole transcriptome profiles to gamete quality. We have developed a new approach to this problem employing artificial neural networks and supervised machine learning with other novel bioinformatics procedures to discover a previously unknown level of ovarian transcriptome function at which minute changes in expression of a few hundred genes is highly predictive of egg quality. In this paper, we briefly review the progress in transcriptomics of fish egg quality and discuss some future directions for this field of study.
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Affiliation(s)
- Craig V Sullivan
- Department of Biology, North Carolina State University, Raleigh, NC 27695-7617, USA; Carolina AquaGyn, P.O. Box 12914, Raleigh, NC 27605, USA(1).
| | - Robert W Chapman
- Marine Resources Division, South Carolina Department of Natural Resources, Charleston, SC 29412, USA
| | - Benjamin J Reading
- Department of Biology, North Carolina State University, Raleigh, NC 27695-7617, USA; Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695-7617, USA(1)
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, Charleston, SC 29424, USA
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Schilling J, Nepomuceno AI, Planchart A, Yoder JA, Kelly RM, Muddiman DC, Daniels HV, Hiramatsu N, Reading BJ. Machine learning reveals sex-specific 17β-estradiol-responsive expression patterns in white perch (Morone americana) plasma proteins. Proteomics 2015; 15:2678-90. [PMID: 25900664 PMCID: PMC5765861 DOI: 10.1002/pmic.201400606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/03/2015] [Accepted: 04/17/2015] [Indexed: 12/29/2022]
Abstract
With growing abundance and awareness of endocrine disrupting compounds (EDCs) in the environment, there is a need for accurate and reliable detection of EDC exposure. Our objective in the present study was to observe differences within and between the global plasma proteomes of sexually mature male and female white perch (Morone americana) before (Initial Control, IC) and after 17β-estradiol (E2 ) induction. Semiquantitative nanoLC-MS/MS data were analyzed by machine learning support vector machines (SVMs) and by two-way ANOVA. By ANOVA, the expression levels of 44, 77, and 57 proteins varied significantly by gender, treatment, and the interaction of gender and treatment, respectively. SVMs perfectly classified male and female perch IC and E2 -induced plasma samples using the protein expression data. E2 -induced male and female perch plasma proteomes contained significantly higher levels of the yolk precursors vitellogenin Aa and Ab (VtgAa, VtgAb), as well as latrophilin and seven transmembrane domain-containing protein 1 (Eltd1) and kininogen 1 (Kng1). This is the first report that Eltd1 and Kng1 may be E2 -responsive proteins in fishes and therefore may be useful indicators of estrogen induction.
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Affiliation(s)
- Justin Schilling
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Angelito I. Nepomuceno
- W. M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Antonio Planchart
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey A. Yoder
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - David C. Muddiman
- W. M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA
| | - Harry V. Daniels
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Naoshi Hiramatsu
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Benjamin J. Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
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Transcriptome Profile Analysis of Ovarian Tissues from Diploid and Tetraploid Loaches Misgurnus anguillicaudatus. Int J Mol Sci 2015; 16:16017-33. [PMID: 26184186 PMCID: PMC4519936 DOI: 10.3390/ijms160716017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/25/2015] [Accepted: 07/08/2015] [Indexed: 01/31/2023] Open
Abstract
RNA sequencing and short-read assembly was utilized to produce a transcriptome of ovarian tissues from three-year-old diploid and tetraploid loaches (Misgurnus anguillicaudatus). A total of 28,369 unigenes were obtained, comprising 10,546 unigenes with length longer than 1000 bp. More than 73% of the unigenes were annotated through sequence comparison with databases. The RNA-seq data revealed that 2253 genes were differentially expressed between diploid and tetraploid loaches, including 1263 up-regulated and 990 down-regulated genes in tetraploid loach. Some differentially expressed genes, such as vitellogenin (Vtg), gonadotropin releasing hormone receptor type A (GnRHRA), steroidogenic acute regulatory protein (StAR), mitogen-activated protein kinase 14a (MAPK14a), ATP synthase subunit alpha (atp5a), and synaptonemal complex protein 1 (Scp1), were involved in regulation of cell proliferation, division, gene transcription, ovarian development and energy metabolism, suggesting that these genes were related to egg diameter of the loach. Results of transcriptome profiling here were validated using real time quantitative PCR in ten selected genes. The present study provided insights into the transcriptome profile of ovarian tissues from diploid and tetraploid loaches Misgurnus anguillicaudatus, which was made available to the research community for functional genomics, comparative genomics, polyploidy evolution and molecular breeding of this loach and other related species.
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Evans TG. Considerations for the use of transcriptomics in identifying the ‘genes that matter’ for environmental adaptation. J Exp Biol 2015; 218:1925-35. [DOI: 10.1242/jeb.114306] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT
Transcriptomics has emerged as a powerful approach for exploring physiological responses to the environment. However, like any other experimental approach, transcriptomics has its limitations. Transcriptomics has been criticized as an inappropriate method to identify genes with large impacts on adaptive responses to the environment because: (1) genes with large impacts on fitness are rare; (2) a large change in gene expression does not necessarily equate to a large effect on fitness; and (3) protein activity is most relevant to fitness, and mRNA abundance is an unreliable indicator of protein activity. In this review, these criticisms are re-evaluated in the context of recent systems-level experiments that provide new insight into the relationship between gene expression and fitness during environmental stress. In general, these criticisms remain valid today, and indicate that exclusively using transcriptomics to screen for genes that underlie environmental adaptation will overlook constitutively expressed regulatory genes that play major roles in setting tolerance limits. Standard practices in transcriptomic data analysis pipelines may also be limiting insight by prioritizing highly differentially expressed and conserved genes over those genes that undergo moderate fold-changes and cannot be annotated. While these data certainly do not undermine the continued and widespread use of transcriptomics within environmental physiology, they do highlight the types of research questions for which transcriptomics is best suited and the need for more gene functional analyses. Such information is pertinent at a time when transcriptomics has become increasingly tractable and many researchers may be contemplating integrating transcriptomics into their research programs.
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