51
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Paterson YZ, Evans N, Kan S, Cribbs A, Henson FMD, Guest DJ. The transcription factor scleraxis differentially regulates gene expression in tenocytes isolated at different developmental stages. Mech Dev 2020; 163:103635. [PMID: 32795590 DOI: 10.1016/j.mod.2020.103635] [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] [Received: 06/01/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 01/01/2023]
Abstract
The transcription factor scleraxis (SCX) is expressed throughout tendon development and plays a key role in directing tendon wound healing. However, little is known regarding its role in fetal or young postnatal tendons, stages in development that are known for their enhanced regenerative capabilities. Here we used RNA-sequencing to compare the transcriptome of adult and fetal tenocytes following SCX knockdown. SCX knockdown had a larger effect on gene expression in fetal tenocytes, affecting 477 genes in comparison to the 183 genes affected in adult tenocytes, indicating that scleraxis-dependent processes may differ in these two developmental stages. Gene ontology, network and pathway analysis revealed an overrepresentation of extracellular matrix (ECM) remodelling processes within both comparisons. These included several matrix metalloproteinases, proteoglycans and collagens, some of which were also investigated in SCX knockdown tenocytes from young postnatal foals. Using chromatin immunoprecipitation, we also identified novel genes that SCX differentially interacts with in adult and fetal tenocytes. These results indicate a role for SCX in modulating ECM synthesis and breakdown and provide a useful dataset for further study into SCX gene regulation.
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Affiliation(s)
- Y Z Paterson
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK.
| | - N Evans
- Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK.
| | - S Kan
- Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK.
| | - A Cribbs
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK.
| | - F M D Henson
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK.
| | - D J Guest
- Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK; Deptartment of Clinical Sciences and Services, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Herts AL9 7TA, UK.
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52
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Harrington AM, Clark KF, Hamlin HJ. Expected ocean warming conditions significantly alter the transcriptome of developing postlarval American lobsters (Homarus americanus): Implications for energetic trade-offs. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100716. [PMID: 32777773 DOI: 10.1016/j.cbd.2020.100716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
The American lobster (Homarus americanus) is one of the most iconic and economically valuable fishery species in the Northwestern Atlantic. Surface ocean temperatures are rapidly increasing across much of the species' range, raising concern about resiliency in the face of environmental change. Warmer temperatures accelerate rates of larval development and enhance survival to the postlarval stage, but the potential costs at the molecular level have rarely been addressed. We explored how exposure to current summer temperatures (16 °C) or temperature regimes mimicking projected moderate or extreme warming scenarios (18 °C and 22 °C, respectively) for the Gulf of Maine during development influences the postlarval lobster transcriptome. After de novo assembling the transcriptome, we identified 2542 differentially expressed (DE; adjusted p < 0.05) transcripts in postlarvae exposed to 16 °C vs. 22 °C, and 422 DE transcripts in postlarvae reared at 16 °C vs. 18 °C. Lobsters reared at 16 °C significantly over-expressed transcripts related to cuticle formation and the immune response up to 14.4- and 8.5-fold respectively, relative to those reared at both 18 °C and 22 °C. In contrast, the expression of transcripts affiliated with metabolism increased up to 7.1-fold as treatment temperature increased. These results suggest that lobsters exposed to projected warming scenarios during development experience a shift in the transcriptome that reflects a potential trade-off between maintaining immune defenses and sustaining increased physiological rates under a warming environment. This could have major implications for post-settlement survival through increased risk of mortality due to disease and/or starvation if energetic demands cannot be met.
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Affiliation(s)
- Amalia M Harrington
- School of Marine Sciences, University of Maine, 5751 Murray Hall, Orono, ME 04469, USA; Aquaculture Research Institute, University of Maine, Orono, ME 04469, USA.
| | - K Fraser Clark
- Department of Animal Sciences and Aquaculture, Faculty of Agriculture, Dalhousie University, 58 Sipu Awti, Bible Hill, NS B2N 5E3, Canada.
| | - Heather J Hamlin
- School of Marine Sciences, University of Maine, 5751 Murray Hall, Orono, ME 04469, USA; Aquaculture Research Institute, University of Maine, Orono, ME 04469, USA.
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53
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Sandoval-Castillo J, Gates K, Brauer CJ, Smith S, Bernatchez L, Beheregaray LB. Adaptation of plasticity to projected maximum temperatures and across climatically defined bioregions. Proc Natl Acad Sci U S A 2020; 117:17112-17121. [PMID: 32647058 PMCID: PMC7382230 DOI: 10.1073/pnas.1921124117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Resilience to environmental stressors due to climate warming is influenced by local adaptations, including plastic responses. The recent literature has focused on genomic signatures of climatic adaptation, but little is known about how plastic capacity may be influenced by biogeographic and evolutionary processes. We investigate phenotypic plasticity as a target of climatic selection, hypothesizing that lineages that evolved in warmer climates will exhibit greater plastic adaptive resilience to upper thermal stress. This was experimentally tested by comparing transcriptomic responses within and among temperate, subtropical, and desert ecotypes of Australian rainbowfish subjected to contemporary and projected summer temperatures. Critical thermal maxima were estimated, and ecological niches delineated using bioclimatic modeling. A comparative phylogenetic expression variance and evolution model was used to assess plastic and evolved changes in gene expression. Although 82% of all expressed genes were found in the three ecotypes, they shared expression patterns in only 5 out of 236 genes that responded to the climate change experiment. A total of 532 genes showed signals of adaptive (i.e., genetic-based) plasticity due to ecotype-specific directional selection, and 23 of those responded to projected summer temperatures. Network analyses demonstrated centrality of these genes in thermal response pathways. The greatest adaptive resilience to upper thermal stress was shown by the subtropical ecotype, followed by the desert and temperate ecotypes. Our findings indicate that vulnerability to climate change will be highly influenced by biogeographic factors, emphasizing the value of integrative assessments of climatic adaptive traits for accurate estimation of population and ecosystem responses.
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Affiliation(s)
| | - Katie Gates
- Molecular Ecology Lab, Flinders University, Bedford Park, SA 5042, Australia
| | - Chris J Brauer
- Molecular Ecology Lab, Flinders University, Bedford Park, SA 5042, Australia
| | - Steve Smith
- Molecular Ecology Lab, Flinders University, Bedford Park, SA 5042, Australia
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
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54
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Studivan MS, Voss JD. Transcriptomic plasticity of mesophotic corals among natural populations and transplants of
Montastraea cavernosa
in the Gulf of Mexico and Belize. Mol Ecol 2020; 29:2399-2415. [DOI: 10.1111/mec.15495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/14/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Michael S. Studivan
- Harbor Branch Oceanographic Institute Florida Atlantic University Fort Pierce FL USA
- Cooperative Institute for Marine and Atmospheric Studies University of Miami Rosenstiel School of Marine and Atmospheric Sciences Miami FL USA
| | - Joshua D. Voss
- Harbor Branch Oceanographic Institute Florida Atlantic University Fort Pierce FL USA
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55
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Liu A, Zhang P, Bai B, Bai F, Jin T, Ren J. Volatile Organic Compounds of Endophytic Burkholderia pyrrocinia Strain JK-SH007 Promote Disease Resistance in Poplar. PLANT DISEASE 2020; 104:1610-1620. [PMID: 32271644 DOI: 10.1094/pdis-11-19-2366-re] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Volatile organic compounds (VOCs) play important roles in the regulation of plant growth and pathogen resistance. However, little is known about the influence of VOCs released from endophytic strains (Burkholderia pyrrocinia strain JK-SH007) on controlling pathogens or inducing systemic resistance in poplar. In this study, we found that VOCs produced by strain JK-SH007 inhibit three poplar canker pathogens (Cytospora chrysosperma, Phomopsis macrospora, and Fusicoccum aesculi) and promote defense enzyme activity and malondialdehyde (MDA) and total phenol (TP) accumulation. Thirteen kinds of VOC components were identified using the solid-phase microextraction combined with gas chromatography-mass spectrometry method. Dimethyl disulfide (DMDS) accounted for the largest proportion of these VOCs. Treatments of poplar seedlings with different volumes of VOC standards (DMDS, benzothiazole, dimethylthiomethane, and phenylacetone) showed that DMDS had the greatest effects on various defense enzyme activities and MDA and TP accumulation. We also found that the inhibitory effect of the VOCs on the three pathogens was gradually enhanced with increasing standard volume. Moreover, the treatment of samples with DMDS significantly reduced the severity and development of the disease caused by three poplar canker pathogens. Comparative transcriptomics analysis of poplar seedlings treated with DMDS showed that there were 1,586 differentially expressed genes in the leaves and stems, and quantitative PCR showed that the gene expression trends were highly consistent with the transcriptome sequencing results. The most significant transcriptomic changes induced by VOCs were related to hormone signal transduction, transcriptional regulation of plant-pathogen interactions, and energy metabolism. Moreover, 137 transcription factors, including members of the ethylene response factor, NAC, WRKY, G2-like, and basic helix-loop-helix protein families, were identified to be involved in the VOC-induced process. This study elucidates the resistance induced by Burkholderia pyrrocinia strain JK-SH007 to poplar canker at the molecular level and can make possible a new method for the comprehensive prevention and control of poplar disease.
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Affiliation(s)
- Ake Liu
- Faculty of Biology Science and Technology, Changzhi University, Shanxi 046011, China
| | - Pengfei Zhang
- Faculty of Biology Science and Technology, Changzhi University, Shanxi 046011, China
| | - Bianxia Bai
- Faculty of Biology Science and Technology, Changzhi University, Shanxi 046011, China
| | - Fenglin Bai
- Faculty of Biology Science and Technology, Changzhi University, Shanxi 046011, China
| | - Tingting Jin
- Faculty of Biology Science and Technology, Changzhi University, Shanxi 046011, China
| | - Jiahong Ren
- Faculty of Biology Science and Technology, Changzhi University, Shanxi 046011, China
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56
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Cunningham CB. Functional genomics of parental care of insects. Horm Behav 2020; 122:104756. [PMID: 32353447 DOI: 10.1016/j.yhbeh.2020.104756] [Citation(s) in RCA: 2] [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: 10/30/2019] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/19/2022]
Abstract
Parental care was likely the first step most lineages made towards sociality. However, the molecular mechanisms that generate parental care are not broadly characterized. Insects are important as an evolutionary independent group from classic models of parental care, such as, house mice. They provide an opportunity to test the generality of our understanding. With this review, I survey the functional genomics of parental care of insects, summarize several recent advances in the broader framework for studying and understanding parental care, and finish with suggested priorities for further research. Although there are too few studies to draw definitive conclusions, I argue that natural selection appears to be rewiring existing gene networks to produce parental care, that the epigenetic mechanisms influencing parental care are not well understood, and, as an interesting early consensus, that genes strongly associated with carer/offspring interactions appear biased towards proteins that are secreted. I summarize the studies that have functionally validate candidate genes and highlight the increasing need to perform this work. I finish with arguments for both conceptual and practical changes moving forward. I argue that future work can increase the use of predictive frameworks, broaden its definition of conservation of mechanism to gene networks rather than single genes, and increase the use of more established comparative methods. I further highlight the practical considerations of standardizing analyses and reporting, increasing the sampling of both carers and offspring, better characterizing gene regulatory networks, better characterizing taxonomically restricted genes and any consistent role they have underpinning parental care, and using factorial designs to disentangle the influence of multiple variables on the expression of parental care.
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57
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Audusseau H, Vandenbulcke F, Dume C, Deschins V, Pauwels M, Gigon A, Bagard M, Dupont L. Impacts of metallic trace elements on an earthworm community in an urban wasteland: Emphasis on the bioaccumulation and genetic characteristics in Lumbricus castaneus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:137259. [PMID: 32105923 DOI: 10.1016/j.scitotenv.2020.137259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
Metallic trace elements (MTEs) soil pollution has become a worldwide concern, particularly regarding its impact on earthworms. Earthworms, which constitute the dominant taxon of soil macrofauna in temperate regions and are crucial ecosystem engineers, are in direct contact with MTEs. The impacts of MTE exposure on earthworms, however, vary by species, with some able to cope with high levels of contamination. We combined different approaches to study the effects of MTEs at different levels of biological organisation of an earthworm community, in a contaminated urban wasteland. Our work is based on field collection of soil and earthworm samples, with a total of 891 adult earthworms from 8 species collected, over 87 quadrats across the study plot. We found that MTE concentrations are highly structured at the plot scale and that some elements, such as Pb, Zn, and Cu, are highly correlated. Comparing species assemblage to MTE concentrations, we found that the juvenile and adult abundances, and community composition, were significantly affected by pollution. Along the pollution gradient, as species richness decreased, Lumbricus castaneus became more dominant. We thus investigated the physiological response of this species to a set of specific elements (Pb, Zn, Cu, and Cd) and studied the impacts of MTE concentrations at the plot scale on its population genetic. These analyses revealed that L. castaneus is able to bioaccumulate high quantities of Cd and Zn, but not of Cu and Pb. The population genetic analysis, based on the genotyping of 175 individuals using 8 microsatellite markers, provided no evidence of the role of the heterogeneity in MTE concentrations as a barrier to gene flow. The multidisciplinary approach we used enabled us to reveal the comparatively high tolerance of L. castaneus to MTE concentrations, suggesting that this is a promising model to study the molecular bases of MTE tolerance.
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Affiliation(s)
- Hélène Audusseau
- Univ. Paris Est Creteil, Sorbonne Université, CNRS, INRA, IRD, Institut d'écologie et des sciences de l'environnement de Paris, 94010 Créteil, France; Department of Zoology, Stockholm University, Stockholm, Sweden; UK Centre for Ecology & Hydrology Maclean Building, Benson Lane, Wallingford, Oxon OX10 8BB, UK.
| | - Franck Vandenbulcke
- Université de Lille, EA 4515-LGCgE - Laboratoire Génie Civil et géo-Environnement, Cité scientifique, SN3, F-59655 Villeneuve d'Ascq, France
| | - Cassandre Dume
- Univ. Paris Est Creteil, Sorbonne Université, CNRS, INRA, IRD, Institut d'écologie et des sciences de l'environnement de Paris, 94010 Créteil, France; Université de Lille, EA 4515-LGCgE - Laboratoire Génie Civil et géo-Environnement, Cité scientifique, SN3, F-59655 Villeneuve d'Ascq, France
| | - Valentin Deschins
- Univ. Paris Est Creteil, Sorbonne Université, CNRS, INRA, IRD, Institut d'écologie et des sciences de l'environnement de Paris, 94010 Créteil, France
| | - Maxime Pauwels
- Université de Lille, CNRS, UMR 8198 - Unité Evolution-Ecologie-Paléontologie, F-59000 Lille, France
| | - Agnès Gigon
- Univ. Paris Est Creteil, Sorbonne Université, CNRS, INRA, IRD, Institut d'écologie et des sciences de l'environnement de Paris, 94010 Créteil, France
| | - Matthieu Bagard
- Univ. Paris Est Creteil, Sorbonne Université, CNRS, INRA, IRD, Institut d'écologie et des sciences de l'environnement de Paris, 94010 Créteil, France
| | - Lise Dupont
- Univ. Paris Est Creteil, Sorbonne Université, CNRS, INRA, IRD, Institut d'écologie et des sciences de l'environnement de Paris, 94010 Créteil, France
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58
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Koch EL, Guillaume F. Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum. PLoS Genet 2020; 16:e1008768. [PMID: 32379753 PMCID: PMC7238888 DOI: 10.1371/journal.pgen.1008768] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 05/19/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Gene expression is known to be highly responsive to the environment and important for adjustment of metabolism but there is also growing evidence that differences in gene regulation contribute to species divergence and differences among locally adapted populations. However, most studies so far investigated populations when divergence had already occurred. Selection acting on expression levels at the onset of adaptation to an environmental change has not been characterized. Understanding the mechanisms is further complicated by the fact that environmental change is often multivariate, meaning that organisms are exposed to multiple stressors simultaneously with potentially interactive effects. Here we use a novel approach by combining fitness and whole-transcriptome data in a large-scale experiment to investigate responses to drought, heat and their combination in Tribolium castaneum. We found that fitness was reduced by both stressors and their combined effect was almost additive. Expression data showed that stressor responses were acting independently and did not interfere physiologically. Since we measured expression and fitness within the same individuals, we were able to estimate selection on gene expression levels. We found that variation in fitness can be attributed to gene expression variation and that selection pressures were environment dependent and opposite between control and stress conditions. We could further show that plastic responses of expression were largely adaptive, i.e. in the direction that should increase fitness.
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Affiliation(s)
- Eva L. Koch
- Department of Evolutionary Biology and Environmental Studies, University
of Zürich, Zürich, Switzerland
- Department of Animal and Plant Science, University of Sheffield, Western
Bank, Sheffield, United Kingdom
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University
of Zürich, Zürich, Switzerland
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59
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Yang L, He T, Xiong F, Chen X, Fan X, Jin S, Geng Z. Identification of key genes and pathways associated with feed efficiency of native chickens based on transcriptome data via bioinformatics analysis. BMC Genomics 2020; 21:292. [PMID: 32272881 PMCID: PMC7146967 DOI: 10.1186/s12864-020-6713-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/01/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Improving feed efficiency is one of the important breeding targets for poultry industry. The aim of current study was to investigate the breast muscle transcriptome data of native chickens divergent for feed efficiency. Residual feed intake (RFI) value was calculated for 1008 closely related chickens. The 5 most efficient (LRFI) and 5 least efficient (HRFI) birds were selected for further analysis. Transcriptomic data were generated from breast muscle collected post-slaughter. RESULTS The differently expressed genes (DEGs) analysis showed that 24 and 325 known genes were significantly up- and down-regulated in LRFI birds. An enrichment analysis of DEGs showed that the genes and pathways related to inflammatory response and immune response were up-regulated in HRFI chickens. Moreover, Gene Set Enrichment Analysis (GSEA) was also employed, which indicated that LRFI chickens increased expression of genes related to mitochondrial function. Furthermore, protein network interaction and function analyses revealed ND2, ND4, CYTB, RAC2, VCAM1, CTSS and TLR4 were key genes for feed efficiency. And the 'phagosome', 'cell adhesion molecules (CAMs)', 'citrate cycle (TCA cycle)' and 'oxidative phosphorylation' were key pathways contributing to the difference in feed efficiency. CONCLUSIONS In summary, a series of key genes and pathways were identified via bioinformatics analysis. These key genes may influence feed efficiency through deep involvement in ROS production and inflammatory response. Our results suggested that LRFI chickens may synthesize ATP more efficiently and control reactive oxygen species (ROS) production more strictly by enhancing the mitochondrial function in skeletal muscle compared with HRFI chickens. These findings provide some clues for understanding the molecular mechanism of feed efficiency in birds and will be a useful reference data for native chicken breeding.
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Affiliation(s)
- Lei Yang
- College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.,Key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Tingting He
- College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.,Key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Fengliang Xiong
- College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China
| | - Xianzhen Chen
- College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.,Key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Xinfeng Fan
- College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.,Key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Sihua Jin
- College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.,Key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China. .,Key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
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60
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Cinel SD, Hahn DA, Kawahara AY. Predator-induced stress responses in insects: A review. JOURNAL OF INSECT PHYSIOLOGY 2020; 122:104039. [PMID: 32113954 DOI: 10.1016/j.jinsphys.2020.104039] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 04/26/2018] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Abstract
Predators can induce extreme stress and profound physiological responses in prey. Insects are the most dominant animal group on Earth and serve as prey for many different predators. Although insects have an extraordinary diversity of anti-predator behavioral and physiological responses, predator-induced stress has not been studied extensively in insects, especially at the molecular level. Here, we review the existing literature on physiological predator-induced stress responses in insects and compare what is known about insect stress to vertebrate stress systems. We conclude that many unrelated insects share a baseline pathway of predator-induced stress responses that we refer to as the octopamine-adipokinetic hormone (OAH) axis. We also present best practices for studying predator-induced stress responses in prey insects. We encourage investigators to compare neurophysiological responses to predator-related stress at the organismal, neurohormonal, tissue, and cellular levels within and across taxonomic groups. Studying stress-response variation between ecological contexts and across taxonomic levels will enable the field to build a holistic understanding of, and distinction between, taxon- and stimulus-specific responses relative to universal stress responses.
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Affiliation(s)
- Scott D Cinel
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
| | - Daniel A Hahn
- Department of Entomology & Nematology, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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61
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Lafuente E, Beldade P. Genomics of Developmental Plasticity in Animals. Front Genet 2019; 10:720. [PMID: 31481970 PMCID: PMC6709652 DOI: 10.3389/fgene.2019.00720] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
Developmental plasticity refers to the property by which the same genotype produces distinct phenotypes depending on the environmental conditions under which development takes place. By allowing organisms to produce phenotypes adjusted to the conditions that adults will experience, developmental plasticity can provide the means to cope with environmental heterogeneity. Developmental plasticity can be adaptive and its evolution can be shaped by natural selection. It has also been suggested that developmental plasticity can facilitate adaptation and promote diversification. Here, we summarize current knowledge on the evolution of plasticity and on the impact of plasticity on adaptive evolution, and we identify recent advances and important open questions about the genomics of developmental plasticity in animals. We give special attention to studies using transcriptomics to identify genes whose expression changes across developmental environments and studies using genetic mapping to identify loci that contribute to variation in plasticity and can fuel its evolution.
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Affiliation(s)
| | - Patrícia Beldade
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- CNRS-UMR5174, Université Paul Sabatier, Toulouse, France
- Centre for Ecology, Evolution, and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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62
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Reisser C, Lo C, Schikorski D, Sham Koua M, Planes S, Ky CL. Strong genetic isolation of the black-lipped pearl oyster (Pinctada margaritifera) in the Marquesas archipelago (French Polynesia). Sci Rep 2019; 9:11420. [PMID: 31388098 PMCID: PMC6684808 DOI: 10.1038/s41598-019-47729-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/23/2019] [Indexed: 11/09/2022] Open
Abstract
The French Polynesian islands are internationally known for their black pearls, produced by culture of the black lipped pearl oyster Pinctada margaritifera. The ongoing development of hatcheries for P. margaritifera in French Polynesia poses new challenges for the industry, particularly regarding the maintenance of genetic diversity in the hatchery stocks. This emphasizes the necessity to characterize the genetic diversity and differentiation within natural and exploited populations, to carefully select putative parental populations. The present study aimed at validating the phylogenetic status and investigating genetic attributes of populations from the only two non-exploited archipelagos of French Polynesia, the Marquesas archipelago, and the Australes archipelago, never analysed before. We found that individuals from both archipelagos belonged to P. margaritifera species. However, while the Australes population was genetically similar to non-exploited populations of the Tuamotu, the Marquesas populations were highly differentiated from the rest of the populations. This differentiation cannot not be only attributed to geographic distance and aquaculture status, but likely to hydrodynamic barriers allowing vicariant events to take place. Our results add up to other studies describing the Marquesas archipelago as a hotspot for biodiversity and differentiation, with some of the highest levels of endemism and vicariance found among marine species worldwide and provide precious information on available genetic resources for the implementation of P. margaritifera selective breeding and its genetic conservation in French Polynesia.
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Affiliation(s)
- Céline Reisser
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, French Polynesia
| | - Cédrik Lo
- Direction des Ressources Marines et Minières, BP 20, 98713 Papeete, Tahiti, French Polynesia
| | - David Schikorski
- Laboratoire Labofarm, 4 Rue Théodore Botrel 22603 Loudeac, Cedex, France
| | - Manaarii Sham Koua
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, French Polynesia
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Labex Corail, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, Cedex, France
| | - Chin-Long Ky
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, French Polynesia.
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Ramírez-Carreto S, Vera-Estrella R, Portillo-Bobadilla T, Licea-Navarro A, Bernaldez-Sarabia J, Rudiño-Piñera E, Verleyen JJ, Rodríguez E, Rodríguez-Almazán C. Transcriptomic and Proteomic Analysis of the Tentacles and Mucus of Anthopleura dowii Verrill, 1869. Mar Drugs 2019; 17:md17080436. [PMID: 31349621 PMCID: PMC6722582 DOI: 10.3390/md17080436] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 02/07/2023] Open
Abstract
Sea anemone venom contains a complex and diverse arsenal of peptides and proteins of pharmacological and biotechnological interest, however, only venom from a few species has been explored from a global perspective to date. In the present study, we identified the polypeptides present in the venom of the sea anemone Anthopleura dowii Verrill, 1869 through a transcriptomic and proteomic analysis of the tentacles and the proteomic profile of the secreted mucus. In our transcriptomic results, we identified 261 polypeptides related to or predicted to be secreted in the venom, including proteases, neurotoxins that could act as either potassium (K+) or sodium (Na+) channels inhibitors, protease inhibitors, phospholipases A2, and other polypeptides. Our proteomic data allowed the identification of 156 polypeptides—48 exclusively identified in the mucus, 20 in the tentacles, and 88 in both protein samples. Only 23 polypeptides identified by tandem mass spectrometry (MS/MS) were related to the venom and 21 exclusively identified in the mucus, most corresponding to neurotoxins and hydrolases. Our data contribute to the knowledge of evolutionary and venomic analyses of cnidarians, particularly of sea anemones.
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Affiliation(s)
- Santos Ramírez-Carreto
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Rosario Vera-Estrella
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Tobías Portillo-Bobadilla
- Unidad de Bioinformática, Bioestadística y Biología Computacional. Red de Apoyo a la Investigación, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México-Instituto Nacional De Ciencias Médicas y Nutrición Salvador Zubirán, Calle Vasco de Quiroga 15, Tlalpan, C.P. 14080, Ciudad de México, México
| | - Alexei Licea-Navarro
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada, BC C.P. 22860, México
| | - Johanna Bernaldez-Sarabia
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada, BC C.P. 22860, México
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Jerome J Verleyen
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Claudia Rodríguez-Almazán
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México.
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Liu C, Oveissi S, Downs R, Kirby J, Nedeva C, Puthalakath H, Faou P, Duan M, Chen W. Semiquantitative Proteomics Enables Mapping of Murine Neutrophil Dynamics following Lethal Influenza Virus Infection. THE JOURNAL OF IMMUNOLOGY 2019; 203:1064-1075. [PMID: 31308090 DOI: 10.4049/jimmunol.1900337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 12/31/2022]
Abstract
Neutrophils are rapidly deployed innate immune cells, and excessive recruitment is causally associated with influenza-induced pathologic conditions. Despite this, the complete set of influenza lethality-associated neutrophil effector proteins is currently unknown. Whether the expression of these proteins is predetermined during bone marrow (BM) neutrophil maturation or further modulated by tissue compartment transitions has also not been comprehensively characterized at a proteome-wide scale. In this study, we used high-resolution mass spectrometry to map how the proteomes of murine neutrophils change comparatively across BM, blood, and the alveolar airspaces to deploy an influenza lethality-associated response. Following lethal influenza infection, mature neutrophils undergo two infection-dependent and one context-independent compartmental transitions. Translation of type I IFN-stimulated genes is first elevated in the BM, preceding the context-independent downregulation of ribosomal proteins observed in blood neutrophils. Following alveolar airspace infiltration, the bronchoalveolar lavage (BAL) neutrophil proteome is further characterized by a limited increase in type I IFN-stimulated and metal-sequestering proteins as well as a decrease in degranulation-associated proteins. An influenza-selective and dose-dependent increase in antiviral and lipid metabolism-associated proteins was also observed in BAL neutrophils, indicative of a modest capacity for pathogen response tuning. Altogether, our study provides new and comprehensive evidence that the BAL neutrophil proteome is shaped by BM neutrophil maturation as well as subsequent compartmental transitions following lethal influenza infection.
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Affiliation(s)
- Chuanxin Liu
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Sara Oveissi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Rachael Downs
- La Trobe Comprehensive Proteomics Platform, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia; and
| | - Jason Kirby
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Urrbrae, South Australia 5064, Australia
| | - Christina Nedeva
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Hamsa Puthalakath
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Pierre Faou
- La Trobe Comprehensive Proteomics Platform, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia; and
| | - Mubing Duan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia;
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia;
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65
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Cholet F, Ijaz UZ, Smith CJ. Differential ratio amplicons (R amp ) for the evaluation of RNA integrity extracted from complex environmental samples. Environ Microbiol 2019; 21:827-844. [PMID: 30585386 PMCID: PMC6392129 DOI: 10.1111/1462-2920.14516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/07/2018] [Accepted: 12/20/2018] [Indexed: 12/31/2022]
Abstract
Reliability and reproducibility of transcriptomics‐based studies are dependent on RNA integrity. In microbial ecology, microfluidics‐based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here, we present an integrity index, the Ratio Amplicon, Ramp, adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the Ramp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA, amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly‐degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT‐Q‐PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this, both the RIN and Ramp are useful, with the Ramp better evaluating mRNA integrity in this study.
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Affiliation(s)
- Fabien Cholet
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Umer Z Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Cindy J Smith
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
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66
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Abstract
In the last decade, the concept of animal stress has been stressed thin to accommodate the effects of short-term changes in cell and tissue physiology, major behavioral syndromes in individuals and ecological disturbances in populations. Seyle's definition of stress as "the nonspecific (common) result of any demand upon the body" now encompasses homeostasis in a broader sense, including all the hierarchical levels in a networked biological system. The heterogeneity of stress responses thus varies within individuals, and stressors become multimodal in terms of typology, source and effects, as well as the responses that each individual elicits to cope with the disturbance. In fish, the time course of changes after stress strongly depends on several factors, including the stressful experiences in early life, the vertical transmission of stressful-prone phenotypes, the degree of individual phenotypic plasticity, the robustness and variety of the epigenetic network related to environmentally induced changes, and the intrinsic behavioral responses (individuality/personality) of each individual. The hierarchical heterogeneity of stress responses demands a code that may decrypt and simplify the analysis of both proximate and evolutionary causes of a particular stress phenotype. We propose an analytical framework, the stressotope, defined as an adaptive scenario dominated by common environmental selective pressures that elicit common multilevel acute stress-induced responses and produce a measurable allostatic load in the organism. The stressotope may constitute a blueprint of embedded interactions between stress-related variations in cell states, molecular mediators and systemic networks, a map of circuits that reflect the inherited and acquired stress responses in an ever-changing, microorganismal-loaded medium. Several features of the proposed model are discussed as a starting point to pin down the maximum common stress responses across immune-neuroendocrine relevant physiological levels and scenarios, including the characterization of behavioral responses, in fish.
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Affiliation(s)
- Joan Carles Balasch
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
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67
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Shin TH, Seo C, Lee DY, Ji M, Manavalan B, Basith S, Chakkarapani SK, Kang SH, Lee G, Paik MJ, Park CB. Silica-coated magnetic nanoparticles induce glucose metabolic dysfunction in vitro via the generation of reactive oxygen species. Arch Toxicol 2019; 93:1201-1212. [DOI: 10.1007/s00204-019-02402-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
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68
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Moretto M, Sonego P, Villaseñor-Altamirano AB, Engelen K. First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_. BMC Bioinformatics 2019; 20:54. [PMID: 30691411 PMCID: PMC6348648 DOI: 10.1186/s12859-019-2643-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/22/2019] [Indexed: 11/30/2022] Open
Abstract
Background Exploring cellular responses to stimuli using extensive gene expression profiles has become a routine procedure performed on a daily basis. Raw and processed data from these studies are available on public databases but the opportunity to fully exploit such rich datasets is limited due to the large heterogeneity of data formats. In recent years, several approaches have been proposed to effectively integrate gene expression data for analysis and exploration at a broader level. Despite the different goals and approaches towards gene expression data integration, the first step is common to any proposed method: data acquisition. Although it is seemingly straightforward to extract valuable information from a set of downloaded files, things can rapidly get complicated, especially as the number of experiments grows. Transcriptomic datasets are deposited in public databases with little regard to data format and thus retrieving raw data might become a challenging task. While for RNA-seq experiments such problem is partially mitigated by the fact that raw reads are generally available on databases such as the NCBI SRA, for microarray experiments standards are not equally well established, or enforced during submission, and thus a multitude of data formats has emerged. Results COMMAND>_ is a specialized tool meant to simplify gene expression data acquisition. It is a flexible multi-user web-application that allows users to search and download gene expression experiments, extract only the relevant information from experiment files, re-annotate microarray platforms, and present data in a simple and coherent data model for subsequent analysis. Conclusions COMMAND>_ facilitates the creation of local datasets of gene expression data coming from both microarray and RNA-seq experiments and may be a more efficient tool to build integrated gene expression compendia. COMMAND>_ is free and open-source software, including publicly available tutorials and documentation.
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Affiliation(s)
- Marco Moretto
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige, Italy.
| | - Paolo Sonego
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Ana B Villaseñor-Altamirano
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma De México, 76230, Juriquilla, Querétaro, Mexico.,Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Kristof Engelen
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige, Italy.
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69
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Chen N, Huang Z, Lu C, Shen Y, Luo X, Ke C, You W. Different Transcriptomic Responses to Thermal Stress in Heat-Tolerant and Heat-Sensitive Pacific Abalones Indicated by Cardiac Performance. Front Physiol 2019; 9:1895. [PMID: 30687115 PMCID: PMC6334008 DOI: 10.3389/fphys.2018.01895] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022] Open
Abstract
The Pacific abalone Haliotis discus hannai is one of the most economically important mollusks in China. Even though it has been farmed in southern China for almost 20 years, summer mortality remains the most challengeable problem for Pacific abalone aquaculture recently. Here, we determined the different heat tolerance ability for five selective lines of H. discus hannai by measuring the cardiac performance and Arrhenius breakpoint temperature (ABT). The Red line (RL) and Yangxia line (YL) were determined as the most heat-sensitive and most heat-tolerant line, respectively. Heart rates for RL were significantly lower than those of the YL at the same temperature (p < 0.05). The differentially expressed genes (DEGs), which were enriched in several pathways including cardiac muscle contraction, glutathione metabolism and oxidative phosphorylation, were identified between RL and YL at control temperature (20°C) and heat stress temperature (28.5°C, the ABT of the RL) by RNA-seq method. In the RL, 3370 DEGs were identified between the control and the heat-stress temperature, while only 1351 DEGs were identified in YL between these two temperature tests. Most of these DEGs were enriched in the pathways such as protein processing in endoplasmic reticulum, nucleotide binding and oligomerization domain (NOD) like receptor signaling, and ubiquitin mediated proteolysis. Notably, the most heat-tolerant line YL used an effective heat-protection strategy based on moderate transcriptional changes and regulation on the expression of key genes.
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Affiliation(s)
- Nan Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Chengkuan Lu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yawei Shen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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70
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Dalziel AC, Laporte M, Guderley H, Bernatchez L. Do differences in the activities of carbohydrate metabolism enzymes between Lake Whitefish ecotypes match predictions from transcriptomic studies? Comp Biochem Physiol B Biochem Mol Biol 2018; 224:138-149. [DOI: 10.1016/j.cbpb.2017.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 11/30/2022]
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71
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Connon RE, Jeffries KM, Komoroske LM, Todgham AE, Fangue NA. The utility of transcriptomics in fish conservation. ACTA ACUST UNITED AC 2018; 221:221/2/jeb148833. [PMID: 29378879 DOI: 10.1242/jeb.148833] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers.
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Affiliation(s)
- Richard E Connon
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba, Canada R3T 2N2
| | - Lisa M Komoroske
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA.,Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Anne E Todgham
- Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Nann A Fangue
- Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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72
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RNA-Seq as an Emerging Tool for Marine Dinoflagellate Transcriptome Analysis: Process and Challenges. Processes (Basel) 2018. [DOI: 10.3390/pr6010005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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73
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Shin TH, Lee DY, Lee HS, Park HJ, Jin MS, Paik MJ, Manavalan B, Mo JS, Lee G. Integration of metabolomics and transcriptomics in nanotoxicity studies. BMB Rep 2018; 51:14-20. [PMID: 29301609 PMCID: PMC5796629 DOI: 10.5483/bmbrep.2018.51.1.237] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Indexed: 12/24/2022] Open
Abstract
Biomedical research involving nanoparticles has produced useful products with medical applications. However, the potential toxicity of nanoparticles in biofluids, cells, tissues, and organisms is a major challenge. The '-omics' analyses provide molecular profiles of multifactorial biological systems instead of focusing on a single molecule. The 'omics' approaches are necessary to evaluate nanotoxicity because classical methods for the detection of nanotoxicity have limited ability in detecting miniscule variations within a cell and do not accurately reflect the actual levels of nanotoxicity. In addition, the 'omics' approaches allow analyses of in-depth changes and compensate for the differences associated with high-throughput technologies between actual nanotoxicity and results from traditional cytotoxic evaluations. However, compared with a single omics approach, integrated omics provides precise and sensitive information by integrating complex biological conditions. Thus, these technologies contribute to extended safety evaluations of nanotoxicity and allow the accurate diagnoses of diseases far earlier than was once possible in the nanotechnology era. Here, we review a novel approach for evaluating nanotoxicity by integrating metabolomics with metabolomic profiling and transcriptomics, which is termed "metabotranscriptomics". [BMB Reports 2018; 51(1): 14-20].
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Affiliation(s)
- Tae Hwan Shin
- Institute of Molecular Science and Technology, Ajou University,
Korea
- Department of Physiology, Ajou University School of Medicine, Suwon 16499,
Korea
| | - Da Yeon Lee
- Department of Physiology, Ajou University School of Medicine, Suwon 16499,
Korea
| | - Hyeon-Seong Lee
- College of Pharmacy, Sunchon National University, Suncheon 57922,
Korea
| | - Hyung Jin Park
- Department of Physiology, Ajou University School of Medicine, Suwon 16499,
Korea
| | - Moon Suk Jin
- Department of Physiology, Ajou University School of Medicine, Suwon 16499,
Korea
| | - Man-Jeong Paik
- College of Pharmacy, Sunchon National University, Suncheon 57922,
Korea
| | | | - Jung-Soon Mo
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499,
Korea
| | - Gwang Lee
- Institute of Molecular Science and Technology, Ajou University,
Korea
- Department of Physiology, Ajou University School of Medicine, Suwon 16499,
Korea
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Giraudo M, Cottin G, Esperanza M, Gagnon P, Silva AOD, Houde M. Transcriptional and cellular effects of benzotriazole UV stabilizers UV-234 and UV-328 in the freshwater invertebrates Chlamydomonas reinhardtii and Daphnia magna. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2017; 36:3333-3342. [PMID: 28708270 DOI: 10.1002/etc.3908] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/16/2017] [Accepted: 07/09/2017] [Indexed: 06/07/2023]
Abstract
Benzotriazole ultra violet stabilizers (BZT-UVs) are compounds used in many applications and products to prevent photochemical degradation. Despite their widespread presence in aquatic ecosystems and persistence in the environment, there are very limited data on their effects and toxicity, and their modes of action remain largely unknown. The objectives of the present study were to evaluate the chronic effects of 2 BZT-UVs, 2-(2H-benzotriazol-2-yl)-4,6-bis(1-methyl-1-phenylethyl)phenol (UV-234) and 2-(2H-benzotriazol-2-yl)-4,6-di-tert-pentylphenol (UV-328), on the freshwater green algae Chlamydomonas reinhardtii and the freshwater crustacean Daphnia magna. Organisms were exposed to 0.01 and 10 μg/L of UV-234, UV-328, as well as a mixture of the 2 compounds. Life-history endpoints (viability, reproduction, and growth) and oxidative stress-related biomarkers (gene transcription, reactive oxygen species [ROS] production, and lipid peroxidation) were measured. Daphnia magna growth, reproduction, and gene transcription were not impacted by 21-d individual or mixed exposure. After 96-h of exposure, no differences were observed on the cellular viability of C. reinhardtii for either of the 2 BZT-UVs. In the algae, results showed increased ROS production in response to UV-328 and lipid peroxidation following exposure to UV-234. Synergistic effects of the 2 BZT-UVs were evident at the transcriptional level with 2 to 6 times up-regulation of glutathione peroxidase (gpx ) in response to the mixture for all treatment conditions. The transcription of superoxide dismutase (sod), catalase (cat), and ascorbic peroxidase (apx) was also regulated by UV-234 and UV-328 in the green algae, most likely as a result of ROS production and lipid peroxidation. Results from the present study suggest potential impacts of UV-234 and UV-328 exposure on the antioxidant defense system in C. reinhardtii. Environ Toxicol Chem 2017;36:3333-3342. © 2017 Crown in the Right of Canada. Published by Wiley Periodicals Inc., on behalf of SETAC.
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Affiliation(s)
- Maeva Giraudo
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Montreal, Quebec, Canada
| | - Guillaume Cottin
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Montreal, Quebec, Canada
- Université Paris Descartes, Paris, France
| | - Marta Esperanza
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Montreal, Quebec, Canada
- Laboratorio de Microbiología, Facultad de Ciencias, Universidad da Coruña and Campus de A Zapateira, A Coruña, Spain
| | - Pierre Gagnon
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Montreal, Quebec, Canada
| | - Amila O De Silva
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Burlington, Ontario, Canada
| | - Magali Houde
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Montreal, Quebec, Canada
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Lockwood BL, Julick CR, Montooth KL. Maternal loading of a small heat shock protein increases embryo thermal tolerance in Drosophila melanogaster. ACTA ACUST UNITED AC 2017; 220:4492-4501. [PMID: 29097593 DOI: 10.1242/jeb.164848] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/02/2017] [Indexed: 01/05/2023]
Abstract
Maternal investment is likely to have direct effects on offspring survival. In oviparous animals whose embryos are exposed to the external environment, maternal provisioning of molecular factors like mRNAs and proteins may help embryos cope with sudden changes in the environment. Here, we sought to modify the maternal mRNA contribution to offspring embryos and test for maternal effects on acute thermal tolerance in early embryos of Drosophila melanogaster We drove in vivo overexpression of a small heat shock protein gene (Hsp23) in female ovaries and measured the effects of acute thermal stress on offspring embryonic survival and larval development. We report that overexpression of the Hsp23 gene in female ovaries produced offspring embryos with increased thermal tolerance. We also found that brief heat stress in the early embryonic stage (0-1 h old) caused decreased larval performance later in life (5-10 days old), as indexed by pupation height. Maternal overexpression of Hsp23 protected embryos against this heat-induced defect in larval performance. Our data demonstrate that transient products of single genes have large and lasting effects on whole-organism environmental tolerance. Further, our results suggest that maternal effects have a profound impact on offspring survival in the context of thermal variability.
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Affiliation(s)
- Brent L Lockwood
- Department of Biology, University of Vermont, Burlington, VT 05405, USA
| | - Cole R Julick
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
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76
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Malek R, Bonnarme P, Irlinger F, Frey-Klett P, Onésime D, Aubert J, Loux V, Beckerich JM. Transcriptomic response of Debaryomyces hansenii during mixed culture in a liquid model cheese medium with Yarrowia lipolytica. Int J Food Microbiol 2017; 264:53-62. [PMID: 29111498 DOI: 10.1016/j.ijfoodmicro.2017.10.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 12/31/2022]
Abstract
Yeasts play a crucial role in cheese ripening. They contribute to the curd deacidification, the establishment of acid-sensitive bacterial communities, and flavour compounds production via proteolysis and catabolism of amino acids (AA). Negative yeast-yeast interaction was observed between the yeast Yarrowia lipolytica 1E07 (YL1E07) and the yeast Debaryomyces hansenii 1L25 (DH1L25) in a model cheese but need elucidation. YL1E07 and DH1L25 were cultivated in mono and co-cultures in a liquid synthetic medium (SM) mimicking the cheese environment and the growth inhibition of DH1L25 in the presence of YL1E07 was reproduced. We carried out microbiological, biochemical (lactose, lactate, AA consumption and ammonia production) and transcriptomic analyses by microarray technology to highlight the interaction mechanisms. We showed that the DH1L25 growth inhibition in the presence of YL1E07 was neither due to the ammonia production nor to the nutritional competition for the medium carbon sources between the two yeasts. The transcriptomic study was the key toward the comprehension of yeast-yeast interaction, and revealed that the inhibition of DH1L25 in co-culture is due to a decrease of the mitochondrial respiratory chain functioning.
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Affiliation(s)
- Reine Malek
- UMR 1319 MICALIS, INRA, AgroParisTech, CBAI, BP01, 78850 Thiverval Grignon, France.
| | - Pascal Bonnarme
- INRA, AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France
| | - Françoise Irlinger
- INRA, AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France
| | - Pascale Frey-Klett
- UMR 1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, 54280 Champenoux, France
| | - Djamila Onésime
- UMR 1319 MICALIS, INRA, AgroParisTech, CBAI, BP01, 78850 Thiverval Grignon, France
| | - Julie Aubert
- UMR 518 Mathématiques et Informatiques Appliquées, AgroParisTech, INRA, 16 rue Claude Bernard, 75231 Paris Cedex 05, France
| | - Valentin Loux
- INRA, Unité Mathématique, Informatique et Génome UR1077, 78352 Jouy-en-Josas, France
| | - Jean-Marie Beckerich
- UMR 1319 MICALIS, INRA, AgroParisTech, CBAI, BP01, 78850 Thiverval Grignon, France
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77
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Transcriptomic response of the Antarctic pteropod Limacina helicina antarctica to ocean acidification. BMC Genomics 2017; 18:812. [PMID: 29061120 PMCID: PMC5653985 DOI: 10.1186/s12864-017-4161-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 10/05/2017] [Indexed: 01/30/2023] Open
Abstract
Background Ocean acidification (OA), a change in ocean chemistry due to the absorption of atmospheric CO2 into surface oceans, challenges biogenic calcification in many marine organisms. Ocean acidification is expected to rapidly progress in polar seas, with regions of the Southern Ocean expected to experience severe OA within decades. Biologically, the consequences of OA challenge calcification processes and impose an energetic cost. Results In order to better characterize the response of a polar calcifier to conditions of OA, we assessed differential gene expression in the Antarctic pteropod, Limacina helicina antarctica. Experimental levels of pCO2 were chosen to create both contemporary pH conditions, and to mimic future pH expected in OA scenarios. Significant changes in the transcriptome were observed when juvenile L. h. antarctica were acclimated for 21 days to low-pH (7.71), mid-pH (7.9) or high-pH (8.13) conditions. Differential gene expression analysis of individuals maintained in the low-pH treatment identified down-regulation of genes involved in cytoskeletal structure, lipid transport, and metabolism. High pH exposure led to increased expression and enrichment for genes involved in shell formation, calcium ion binding, and DNA binding. Significant differential gene expression was observed in four major cellular and physiological processes: shell formation, the cellular stress response, metabolism, and neural function. Across these functional groups, exposure to conditions that mimic ocean acidification led to rapid suppression of gene expression. Conclusions Results of this study demonstrated that the transcriptome of the juvenile pteropod, L. h. antarctica, was dynamic and changed in response to different levels of pCO2. In a global change context, exposure of L. h. antarctica to the low pH, high pCO2 OA conditions resulted in a suppression of transcripts for genes involved in key physiological processes: calcification, metabolism, and the cellular stress response. The transcriptomic response at both acute and longer-term acclimation time frames indicated that contemporary L. h. antarctica may not have the physiological plasticity necessary for adaptation to OA conditions expected in future decades. Lastly, the differential gene expression results further support the role of shelled pteropods such as L. h. antarctica as sentinel organisms for the impacts of ocean acidification. Electronic supplementary material The online version of this article (10.1186/s12864-017-4161-0) contains supplementary material, which is available to authorized users.
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78
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Oomen RA, Hutchings JA. Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing. Facets (Ott) 2017. [DOI: 10.1139/facets-2017-0015] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.
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Affiliation(s)
- Rebekah A. Oomen
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Institute of Marine Research, Flødevigen Research Station, 4817 His, Norway
| | - Jeffrey A. Hutchings
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Institute of Marine Research, Flødevigen Research Station, 4817 His, Norway
- Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway
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79
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A Model of Exposure to Extreme Environmental Heat Uncovers the Human Transcriptome to Heat Stress. Sci Rep 2017; 7:9429. [PMID: 28842615 PMCID: PMC5573409 DOI: 10.1038/s41598-017-09819-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 07/31/2017] [Indexed: 12/20/2022] Open
Abstract
The molecular mechanisms by which individuals subjected to environmental heat stress either recover or develop heat-related complications are not well understood. We analysed the changes in blood mononuclear gene expression patterns in human volunteers exposed to extreme heat in a sauna (temperature of 75.7 ± 0.86 °C). Our analysis reveals that expression changes occur rapidly with no significant increase in core temperature and continue to amplify one hour after the end of heat stress. The reprogramed transcriptome was predominantly inhibitory, as more than two-thirds of the expressed genes were suppressed. The differentially expressed genes encoded proteins that function in stress-associated pathways; including proteostasis, energy metabolism, cell growth and proliferation, and cell death, and survival. The transcriptome also included mitochondrial dysfunction, altered protein synthesis, and reduced expression of genes -related to immune function. The findings reveal the human transcriptomic response to heat and highlight changes that might underlie the health outcomes observed during heat waves.
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80
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Bailey A, De Wit P, Thor P, Browman HI, Bjelland R, Shema S, Fields DM, Runge JA, Thompson C, Hop H. Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO 2-acidified sea water. Ecol Evol 2017; 7:7145-7160. [PMID: 28944006 PMCID: PMC5606855 DOI: 10.1002/ece3.3063] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/10/2017] [Accepted: 04/16/2017] [Indexed: 01/03/2023] Open
Abstract
Ocean acidification is the increase in seawater pCO 2 due to the uptake of atmospheric anthropogenic CO 2, with the largest changes predicted to occur in the Arctic seas. For some marine organisms, this change in pCO 2, and associated decrease in pH, represents a climate change-related stressor. In this study, we investigated the gene expression patterns of nauplii of the Arctic copepod Calanus glacialis cultured at low pH levels. We have previously shown that organismal-level performance (development, growth, respiration) of C. glacialis nauplii is unaffected by low pH. Here, we investigated the molecular-level response to lowered pH in order to elucidate the physiological processes involved in this tolerance. Nauplii from wild-caught C. glacialis were cultured at four pH levels (8.05, 7.9, 7.7, 7.5). At stage N6, mRNA was extracted and sequenced using RNA-seq. The physiological functionality of the proteins identified was categorized using Gene Ontology and KEGG pathways. We found that the expression of 151 contigs varied significantly with pH on a continuous scale (93% downregulated with decreasing pH). Gene set enrichment analysis revealed that, of the processes downregulated, many were components of the universal cellular stress response, including DNA repair, redox regulation, protein folding, and proteolysis. Sodium:proton antiporters were among the processes significantly upregulated, indicating that these ion pumps were involved in maintaining cellular pH homeostasis. C. glacialis significantly alters its gene expression at low pH, although they maintain normal larval development. Understanding what confers tolerance to some species will support our ability to predict the effects of future ocean acidification on marine organisms.
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Affiliation(s)
- Allison Bailey
- Norwegian Polar Institute Tromsø Norway.,Department of Arctic and Marine Biology Faculty of Biosciences Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Pierre De Wit
- University of Gothenburg Department of Marine Sciences Sven Lovén Centre for Marine Sciences Tjärnö Sweden
| | | | - Howard I Browman
- Austevoll Research Station Institute of Marine Research Storebø Norway
| | - Reidun Bjelland
- Austevoll Research Station Institute of Marine Research Storebø Norway
| | - Steven Shema
- Austevoll Research Station Institute of Marine Research Storebø Norway
| | - David M Fields
- Bigelow Laboratory for Ocean Sciences East Boothbay ME USA
| | - Jeffrey A Runge
- Gulf of Maine Research Institute University of Maine Orono ME USA
| | - Cameron Thompson
- Gulf of Maine Research Institute University of Maine Orono ME USA
| | - Haakon Hop
- Norwegian Polar Institute Tromsø Norway.,Department of Arctic and Marine Biology Faculty of Biosciences Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
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81
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Abstract
Background Transcriptomic approaches (microarray and RNA-seq) have been a tremendous advance for molecular science in all disciplines, but they have made interpretation of hypothesis testing more difficult because of the large number of comparisons that are done within an experiment. The result has been a proliferation of techniques aimed at solving the multiple comparisons problem, techniques that have focused primarily on minimizing Type I error with little or no concern about concomitant increases in Type II errors. We have previously proposed a novel approach for setting statistical thresholds with applications for high throughput omics-data, optimal α, which minimizes the probability of making either error (i.e. Type I or II) and eliminates the need for post-hoc adjustments. Results A meta-analysis of 242 microarray studies extracted from the peer-reviewed literature found that current practices for setting statistical thresholds led to very high Type II error rates. Further, we demonstrate that applying the optimal α approach results in error rates as low or lower than error rates obtained when using (i) no post-hoc adjustment, (ii) a Bonferroni adjustment and (iii) a false discovery rate (FDR) adjustment which is widely used in transcriptome studies. Conclusions We conclude that optimal α can reduce error rates associated with transcripts in both microarray and RNA-seq experiments, but point out that improved statistical techniques alone cannot solve the problems associated with high throughput datasets – these approaches need to be coupled with improved experimental design that considers larger sample sizes and/or greater study replication. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1728-3) contains supplementary material, which is available to authorized users.
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82
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Voelckel C, Gruenheit N, Lockhart P. Evolutionary Transcriptomics and Proteomics: Insight into Plant Adaptation. TRENDS IN PLANT SCIENCE 2017; 22:462-471. [PMID: 28365131 DOI: 10.1016/j.tplants.2017.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/21/2017] [Accepted: 03/01/2017] [Indexed: 06/07/2023]
Abstract
Comparative transcriptomics and proteomics (T&P) have brought biological insight into development, gene function, and physiological stress responses. However, RNA-seq and high-throughput proteomics remain underutilised in studies of plant adaptation. These methodologies have created discovery tools with the potential to significantly advance our understanding of adaptive diversification. We outline experimental recommendations for their application. We discuss analysis models and approaches that accelerate the identification of adaptive gene sets and integrate transcriptome, proteome, phenotypic, and environmental data. Finally, we encourage widespread uptake and future developments in T&P that will advance our understanding of evolution and adaptation.
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Affiliation(s)
| | - Nicole Gruenheit
- Faculty of Biology, Health, and Medicine, University of Manchester, Manchester, UK
| | - Peter Lockhart
- Institute for Fundamental Sciences, Massey University, Palmerston North, New Zealand
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83
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Evans TG, Pespeni MH, Hofmann GE, Palumbi SR, Sanford E. Transcriptomic responses to seawater acidification among sea urchin populations inhabiting a natural pH mosaic. Mol Ecol 2017; 26:2257-2275. [PMID: 28141889 DOI: 10.1111/mec.14038] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 01/07/2023]
Abstract
Increasing awareness of spatial and temporal variation in ocean pH suggests some marine populations may be adapted to local pH regimes and will therefore respond differently to present-day pH variation and to long-term ocean acidification. In the Northeast Pacific Ocean, differences in the strength of coastal upwelling cause latitudinal variation in prevailing pH regimes that are hypothesized to promote local adaptation and unequal pH tolerance among resident populations. In this study, responses to experimental seawater acidification were compared among embryos and larvae from six populations of purple sea urchins (Strongylocentrotus purpuratus) inhabiting areas that differ in their frequency of low pH exposure and that prior research suggests are locally adapted to seawater pH. Transcriptomic analyses demonstrate urchin populations most frequently exposed to low pH seawater responded to experimental acidification by expressing genes within major ATP-producing pathways at greater levels than populations encountering low pH less often. Multiple genes within the tricarboxylic acid cycle, electron transport chain and fatty acid beta oxidation pathways were upregulated in urchin populations experiencing low pH conditions most frequently. These same metabolic pathways were significantly over-represented among genes both expressed in a population-specific manner and putatively under selection to enhance low pH tolerance. Collectively, these data suggest natural selection is acting on metabolic gene networks to redirect ATP toward maintaining acid-base homeostasis and enhance tolerance of seawater acidification. As a trade-off, marine populations more tolerant of low pH may have less energy to put towards other aspects of fitness and to respond to additional ocean change.
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Affiliation(s)
- Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA
| | - Melissa H Pespeni
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Stephen R Palumbi
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, 93950, USA
| | - Eric Sanford
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA, 94923, USA
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84
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Adamo SA. Stress responses sculpt the insect immune system, optimizing defense in an ever-changing world. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 66:24-32. [PMID: 27288849 DOI: 10.1016/j.dci.2016.06.005] [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: 11/05/2015] [Revised: 06/03/2016] [Accepted: 06/07/2016] [Indexed: 06/06/2023]
Abstract
A whole organism, network approach can help explain the adaptive purpose of stress-induced changes in immune function. In insects, mediators of the stress response (e.g. stress hormones) divert molecular resources away from immune function and towards tissues necessary for fight-or-flight behaviours. For example, molecules such as lipid transport proteins are involved in both the stress and immune responses, leading to a reduction in disease resistance when these proteins are shifted towards being part of the stress response system. Stress responses also alter immune system strategies (i.e. reconfiguration) to compensate for resource losses that occur during fight-or flight events. In addition, stress responses optimize immune function for different physiological conditions. In insects, the stress response induces a pro-inflammatory state that probably enhances early immune responses.
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Affiliation(s)
- Shelley Anne Adamo
- Dept. Psychology and Neuroscience, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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85
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Hawkins TD, Warner ME. Warm preconditioning protects against acute heat-induced respiratory dysfunction and delays bleaching in a symbiotic sea anemone. ACTA ACUST UNITED AC 2016; 220:969-983. [PMID: 27980125 DOI: 10.1242/jeb.150391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/08/2016] [Indexed: 12/18/2022]
Abstract
Preconditioning to non-stressful warming can protect some symbiotic cnidarians against the high temperature-induced collapse of their mutualistic endosymbiosis with photosynthetic dinoflagellates (Symbiodinium spp.), a process known as bleaching. Here, we sought to determine whether such preconditioning is underpinned by differential regulation of aerobic respiration. We quantified in vivo metabolism and mitochondrial respiratory enzyme activity in the naturally symbiotic sea anemone Exaiptasia pallida preconditioned to 30°C for >7 weeks as well as anemones kept at 26°C. Preconditioning resulted in increased Symbiodinium photosynthetic activity and holobiont (host+symbiont) respiration rates. Biomass-normalised activities of host respiratory enzymes [citrate synthase and the mitochondrial electron transport chain (mETC) complexes I and IV] were higher in preconditioned animals, suggesting that increased holobiont respiration may have been due to host mitochondrial biogenesis and/or enlargement. Subsequent acute heating of preconditioned and 'thermally naive' animals to 33°C induced dramatic increases in host mETC complex I and Symbiodinium mETC complex II activities only in thermally naive E. pallida These changes were not reflected in the activities of other respiratory enzymes. Furthermore, bleaching in preconditioned E. pallida (defined as the significant loss of symbionts) was delayed by several days relative to the thermally naive group. These findings suggest that changes to mitochondrial biogenesis and/or function in symbiotic cnidarians during warm preconditioning might play a protective role during periods of exposure to stressful heating.
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Affiliation(s)
- Thomas D Hawkins
- School of Marine Science and Policy, College of Earth, Ocean and Environment, University of Delaware, 700 Pilottown Road, Lewes, DE 19958, USA
| | - Mark E Warner
- School of Marine Science and Policy, College of Earth, Ocean and Environment, University of Delaware, 700 Pilottown Road, Lewes, DE 19958, USA
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86
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Clemson AS, Sgrò CM, Telonis-Scott M. Thermal plasticity in Drosophila melanogaster populations from eastern Australia: quantitative traits to transcripts. J Evol Biol 2016; 29:2447-2463. [PMID: 27542565 DOI: 10.1111/jeb.12969] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/19/2016] [Accepted: 08/17/2016] [Indexed: 12/19/2022]
Abstract
The flexibility afforded to genotypes in different environments by phenotypic plasticity is of interest to biologists studying thermal adaptation because of the thermal lability of many traits. Differences in thermal performance and reaction norms can provide insight into the evolution of thermal adaptation to explore broader questions such as species distributions and persistence under climate change. One approach is to study the effects of temperature on fitness, morphological and more recently gene expression traits in populations from different climatic origins. The diverse climatic conditions experienced by Drosophila melanogaster along the eastern Australian temperate-tropical gradient are ideal given the high degree of continuous trait differentiation, but reaction norm variation has not been well studied in this system. Here, we reared a tropical and temperate population from the ends of the gradient over six developmental temperatures and examined reaction norm variation for five quantitative traits including thermal performance for fecundity, and reaction norms for thermotolerance, body size, viability and 23 transcript-level traits. Despite genetic variation for some quantitative traits, we found no differentiation between the populations for fecundity thermal optima and breadth, and the reaction norms for the other traits were largely parallel, supporting previous work suggesting that thermal evolution occurs by changes in trait means rather than by reaction norm shifts. We examined reaction norm variation in our expanded thermal regime for a gene set shown to previously exhibit GxE for expression plasticity in east Australian flies, as well as key heat-shock genes. Although there were differences in curvature between the populations suggesting a higher degree of thermal plasticity in expression patterns than for the quantitative traits, we found little evidence to support a role for genetic variation in maintaining expression plasticity.
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Affiliation(s)
- A S Clemson
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - C M Sgrò
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - M Telonis-Scott
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
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87
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Cammen KM, Andrews KR, Carroll EL, Foote AD, Humble E, Khudyakov JI, Louis M, McGowen MR, Olsen MT, Van Cise AM. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. J Hered 2016; 107:481-95. [PMID: 27511190 DOI: 10.1093/jhered/esw044] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022] Open
Abstract
The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.
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Affiliation(s)
- Kristina M Cammen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise).
| | - Kimberly R Andrews
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emma L Carroll
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Andrew D Foote
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emily Humble
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Jane I Khudyakov
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Marie Louis
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Michael R McGowen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Morten Tange Olsen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Amy M Van Cise
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
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88
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Papetti C, Lucassen M, Pörtner HO. Integrated studies of organismal plasticity through physiological and transcriptomic approaches: examples from marine polar regions. Brief Funct Genomics 2016; 15:365-72. [PMID: 27345433 DOI: 10.1093/bfgp/elw024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transcriptomic methods are now widely used in functional genomic research. The vast amount of information received from these studies comes along with the challenge of developing a precise picture of the functional consequences and the characteristic regulatory mechanisms. Here we assess recent studies in marine species and their adaptation to polar (and seasonal) cold and explore how they have been able to draw reliable conclusions from transcriptomic patterns on functional consequences in the organisms. Our analysis indicates that the interpretation of transcriptomic data suffers from insufficient understanding of the consequences for whole organism performance and fitness and comes with the risk of supporting only preliminary and superficial statements.We propose that the functional understanding of transcriptomic data may be improved by their tighter integration into overarching physiological concepts that support the more specific interpretation of the 'omics' data and, at the same time, can be developed further through embedding the transcriptomic phenomena observed. Such possibilities have not been fully exploited.In the context of thermal adaptation and limitation, we explore preliminary evidence that the concept of oxygen and capacity limited thermal tolerance (OCLTT) may provide sufficient complexity to guide the integration of such data and the development of associated functional hypotheses. At the same time, we identify a lack of methodological approaches linking genes and function to higher levels of integration, in terms of organism and ecosystem functioning, at temporal and geographical scales, to support more reliable conclusions and be predictive with respect to the effects of global changes.
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89
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McCairns RJS, Smith S, Sasaki M, Bernatchez L, Beheregaray LB. The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes. Evol Appl 2016; 9:531-45. [PMID: 27099620 PMCID: PMC4831457 DOI: 10.1111/eva.12363] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/14/2016] [Indexed: 12/14/2022] Open
Abstract
Whilst adaptation and phenotypic plasticity might buffer species against habitat degradation associated with global climate change, few studies making such claims also possess the necessary and sufficient data to support them. Doing so requires demonstration of heritable variation in traits affecting fitness under new environmental conditions. We address this issue using an emerging aquatic system to study adaptation to climate change, the crimson-spotted rainbowfish (Melanotaenia duboulayi), a freshwater species from a region of eastern Australia projected to be affected by marked temperature increases. Captive born M. duboulayi of known pedigree were used to assess the long-term effects of contemporary and 2070-projected summer temperatures on the expression of genes previously identified in a climate change transcriptomics (RNA-Seq) experiment. Nearly all genes responded to increasing temperature. Significant additive genetic variance explained a moderate proportion of transcriptional variation for all genes. Most genes also showed broad-sense genetic variation in transcriptional plasticity. Additionally, molecular pathways of candidate genes co-occur with genes inferred to be under climate-mediated selection in wild M. duboulayi populations. Together, these results indicate the presence of existing variation in important physiological traits, and the potential for adaptive responses to a changing thermal environment.
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Affiliation(s)
- R. J. Scott McCairns
- Molecular Ecology LaboratoryFlinders UniversityAdelaideSAAustralia
- Centre National de la Recherche ScientifiqueUMR 7263 (IMBE) Institut Méditerranéen de la Biodiversité et d'Ecologie Marine et ContinentaleMarseilleFrance
| | - Steve Smith
- Molecular Ecology LaboratoryFlinders UniversityAdelaideSAAustralia
- Department of Integrative Biology and EvolutionUniversity of Veterinary MedicineViennaAustria
| | - Minami Sasaki
- Molecular Ecology LaboratoryFlinders UniversityAdelaideSAAustralia
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQCCanada
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90
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Population-specific renal proteomes of marine and freshwater three-spined sticklebacks. J Proteomics 2016; 135:112-131. [DOI: 10.1016/j.jprot.2015.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/16/2015] [Accepted: 10/02/2015] [Indexed: 12/20/2022]
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91
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Selection of best-performing reference gene products for investigating transcriptional regulation across silvering in the European eel (Anguilla anguilla). Sci Rep 2015; 5:16966. [PMID: 26593703 PMCID: PMC4655329 DOI: 10.1038/srep16966] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/22/2015] [Indexed: 12/05/2022] Open
Abstract
The focus of the present study was to set a methodological approach for evaluating molecular mechanisms underlying silvering transformation in the European eel, Anguilla anguilla. Silvering is a tightly controlled process during which eels undergo significant morphological, physiological and behavioral changes, pre-adapting for the oceanic spawning migration. Female eels showing different silver indexes were caught in different seasons in the Comacchio Lagoon (North Adriatic Sea, Italy). Isolated hepatocytes from these eels were selected as the experimental model given the relevant role of these cells in metabolic functions potentially altered during silvering. Expression profiles of 7 candidate reference transcripts were analyzed seeking the most viable and robust strategies for accurate qPCR data normalization during silvering. Stability analysis and further statistical validation identified transcripts encoding the ribosomal proteins L13 and ARP as the appropriate reference genes in studies on A. anguilla through silvering. The identified reference transcripts were further used to evaluate expression profiles of target transcripts encoding the thyroid hormone receptor β (THRβ) and vitellogenin (vtg), known to be involved in silvering processes. To the best of our knowledge, this is the first study comparing THRβ expression in European eels across silvering.
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92
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Evans TG, Padilla-Gamiño JL, Kelly MW, Pespeni MH, Chan F, Menge BA, Gaylord B, Hill TM, Russell AD, Palumbi SR, Sanford E, Hofmann GE. Ocean acidification research in the 'post-genomic' era: Roadmaps from the purple sea urchin Strongylocentrotus purpuratus. Comp Biochem Physiol A Mol Integr Physiol 2015; 185:33-42. [PMID: 25773301 DOI: 10.1016/j.cbpa.2015.03.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/07/2015] [Accepted: 03/08/2015] [Indexed: 01/26/2023]
Abstract
Advances in nucleic acid sequencing technology are removing obstacles that historically prevented use of genomics within ocean change biology. As one of the first marine calcifiers to have its genome sequenced, purple sea urchins (Strongylocentrotus purpuratus) have been the subject of early research exploring genomic responses to ocean acidification, work that points to future experiments and illustrates the value of expanding genomic resources to other marine organisms in this new 'post-genomic' era. This review presents case studies of S. purpuratus demonstrating the ability of genomic experiments to address major knowledge gaps within ocean acidification. Ocean acidification research has focused largely on species vulnerability, and studies exploring mechanistic bases of tolerance toward low pH seawater are comparatively few. Transcriptomic responses to high pCO₂ seawater in a population of urchins already encountering low pH conditions have cast light on traits required for success in future oceans. Secondly, there is relatively little information on whether marine organisms possess the capacity to adapt to oceans progressively decreasing in pH. Genomics offers powerful methods to investigate evolutionary responses to ocean acidification and recent work in S. purpuratus has identified genes under selection in acidified seawater. Finally, relatively few ocean acidification experiments investigate how shifts in seawater pH combine with other environmental factors to influence organism performance. In S. purpuratus, transcriptomics has provided insight into physiological responses of urchins exposed simultaneously to warmer and more acidic seawater. Collectively, these data support that similar breakthroughs will occur as genomic resources are developed for other marine species.
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Affiliation(s)
- Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, CA 94542, USA.
| | | | - Morgan W Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Melissa H Pespeni
- Department of Biology, University of Vermont, Burlington, VT 05405, USA
| | - Francis Chan
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331-2914, USA
| | - Bruce A Menge
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331-2914, USA
| | - Brian Gaylord
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Tessa M Hill
- Department of Geology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Ann D Russell
- Department of Geology, University of California Davis, Davis, CA 95616, USA
| | - Stephen R Palumbi
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Eric Sanford
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, USA
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