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George MN, Cattau O, Middleton MA, Lawson D, Vadopalas B, Gavery M, Roberts SB. Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Glob Chang Biol 2023; 29:6969-6987. [PMID: 37464471 DOI: 10.1111/gcb.16880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/20/2023]
Abstract
Polyploidy has been suggested to negatively impact environmental stress tolerance, resulting in increased susceptibility to extreme climate events. In this study, we compared the genomic and physiological response of diploid (2n) and triploid (3n) Pacific oysters (Crassostrea gigas) to conditions present during an atmospheric heatwave that impacted the Pacific Northwestern region of the United States in the summer of 2021. Climate stressors were applied either singly (single stressor; elevated seawater temperature, 30°C) or in succession (multiple stressor; elevated seawater temperature followed by aerial emersion at 44°C), replicating conditions present within the intertidal over a tidal cycle during the event. Oyster mortality rate was elevated within stress treatments with respect to the control and was significantly higher in triploids than diploids following multiple stress exposure (36.4% vs. 14.8%). Triploids within the multiple stressor treatment exhibited signs of energetic limitation, including metabolic depression, a significant reduction in ctenidium Na+ /K+ ATPase activity, and the dysregulated expression of genes associated with stress response, innate immunity, glucose metabolism, and mitochondrial function. Functional enrichment analysis of ploidy-specific gene sets identified that biological processes associated with metabolism, stress tolerance, and immune function were overrepresented within triploids across stress treatments. Our results suggest that triploidy impacts the transcriptional regulation of key processes that underly the stress response of Pacific oysters, resulting in downstream shifts in physiological tolerance limits that may increase susceptibility to extreme climate events that present multiple environmental stressors. The impact of chromosome set manipulation on the climate resilience of marine organisms has important implications for domestic food security within future climate scenarios, especially as triploidy induction becomes an increasingly popular tool to elicit reproductive control across a wide range of species used within marine aquaculture.
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Affiliation(s)
- Matthew N George
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, USA
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Olivia Cattau
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Mollie A Middleton
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
- Saltwater Inc., Anchorage, Alaska, USA
| | - Delaney Lawson
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Brent Vadopalas
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Mackenzie Gavery
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, USA
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2
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Arredondo-Espinoza R, Ibarra AM, Roberts SB, Sicard-González MT, Escobedo-Fregoso C. Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge. Comp Biochem Physiol Part D Genomics Proteomics 2023; 47:101089. [PMID: 37269757 DOI: 10.1016/j.cbd.2023.101089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/05/2023]
Abstract
Since the introduction of the Pacific oyster Crassostrea gigas in Baja California Sur, Mexico, its culture has faced environmental challenges, specifically increasing temperatures that result in high mortalities. The inter-tidal zone seawater temperature during a year at the Baja California Peninsula broadly ranges from 7 °C to 39 °C. Therefore, to understand how oysters respond to heat stress during daily temperature oscillations, heat-resistant (RR, father, and mother resistant) and heat-susceptible (SS, both parents susceptible) phenotypes families from a C. gigas breeding program were exposed to a thermal challenge. Based on a laboratory-simulated daily oscillatory thermal challenge (26 to 34 °C) for 30 days, RR phenotype presented differences compared to SS phenotype since the beginning (day 0) of the thermal challenge. Gene expression analyses revealed 1822 differentially expressed up-regulated transcripts in RR, related to functions of metabolic processes, biological regulation, and response to stimulus and signaling. At the end of the experiment (day 30), 2660 differentially expressed up-regulated transcripts were identified in RR. Functional analysis of the genes expressed indicates responses of regulation of biological processes and response to a stimulus. Additionally, 340 genes were differentially expressed among RR vs. SS from the beginning to the end of the thermal challenge, where 170 genes were up-regulated, and 170 were down-regulated. These transcriptomic profiles represent the first report to identify gene expression markers associated with RR phenotypes for the Pacific oyster to the future broodstock selection.
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Affiliation(s)
- Roberto Arredondo-Espinoza
- Centro de Investigaciones Biológicas del Noroeste S.C. (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, Baja California Sur, Mexico
| | - Ana M Ibarra
- Centro de Investigaciones Biológicas del Noroeste S.C. (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, Baja California Sur, Mexico
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA. https://twitter.com/sr320
| | - Maria Teresa Sicard-González
- Centro de Investigaciones Biológicas del Noroeste S.C. (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, Baja California Sur, Mexico
| | - Cristina Escobedo-Fregoso
- Consejo Nacional de Ciencia y Tecnología-Centro de Investigaciones Biológicas del Noroeste S.C. (CONACYT-CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, Baja California Sur, Mexico.
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3
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Wanamaker SA, Mitchell KR, Thompson RE, Eudeline B, Vadopalas B, Timmins-Schiffman EB, Roberts SB. Correction: Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc. BMC Genomics 2023; 24:188. [PMID: 37024775 PMCID: PMC10080924 DOI: 10.1186/s12864-023-09145-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Affiliation(s)
- Shelly A Wanamaker
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, 98105, USA.
| | - Kaitlyn R Mitchell
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, 98105, USA
| | - Rhonda Elliott Thompson
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, 98105, USA
| | | | - Brent Vadopalas
- Washington Sea Grant, University of Washington, Seattle, Washington, USA
| | | | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, 98105, USA
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Silliman K, Spencer LH, White SJ, Roberts SB. Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate. Genome Biol Evol 2023; 15:evad013. [PMID: 36740242 PMCID: PMC10468963 DOI: 10.1093/gbe/evad013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 01/10/2023] [Accepted: 01/24/2023] [Indexed: 02/07/2023] Open
Abstract
Delineating the relative influence of genotype and the environment on DNA methylation is critical for characterizing the spectrum of organism fitness as driven by adaptation and phenotypic plasticity. In this study, we integrated genomic and DNA methylation data for two distinct Olympia oyster (Ostrea lurida) populations while controlling for within-generation environmental influences. In addition to providing the first characterization of genome-wide DNA methylation patterns in the oyster genus Ostrea, we identified 3,963 differentially methylated loci between populations. Our results show a clear coupling between genetic and epigenetic patterns of variation, with 27% of variation in interindividual methylation differences explained by genotype. Underlying this association are both direct genetic changes in CpGs (CpG-SNPs) and genetic variation with indirect influence on methylation (mQTLs). When comparing measures of genetic and epigenetic population divergence at specific genomic regions this relationship surprisingly breaks down, which has implications for the methods commonly used to study epigenetic and genetic coupling in marine invertebrates.
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Affiliation(s)
- Katherine Silliman
- South Carolina Department of Natural Resources, Marine Resources Research
Institute, Charleston, South Carolina
| | - Laura H Spencer
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
| | - Samuel J White
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
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Dang X, Lim YK, Li Y, Roberts SB, Li L, Thiyagarajan V. Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment. Mol Ecol 2023; 32:412-427. [PMID: 36314404 DOI: 10.1111/mec.16751] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/22/2022]
Abstract
For marine invertebrates with a pelagic-benthic life cycle, larval exposure to ocean acidification (OA) can affect adult performance in response to another environmental stressor. This carry-over effect has the potential to alter phenotypic traits. However, the molecular mechanisms that mediate "OA"-triggered carry-over effects have not been explored despite such information being key to improving species fitness and management strategies for aquafarming. This study integrated the genome-wide DNA methylome and transcriptome to examine epigenetic modification-mediated carry-over OA impacts on phenotypic traits of the ecologically and commercially important oyster species Crassostrea hongkongensis under field conditions. Larvae of C. hongkongensis were exposed to control pH 8.0 and low pH 7.4 conditions, mimicking near future OA scenario in their habitat, before being outplanted as post-metamorphic juveniles at two mariculture field sites with contrasting environmental stressors for 9 months. The larval carry-over OA effect was found to have persistent impacts on the growth and survival trade-off traits on the outplanted juveniles, although the beneficial or adverse effect depended on the environmental conditions at the outplanted sites. Site-specific plasticity was demonstrated with a diverse DNA methylation-associated gene expression profile, with signal transduction and the endocrine system being the most common and highly enriched functions. Highly methylated exons prevailed in the key genes related to general metabolic and endocytic responses and these genes are evolutionarily conserved in various marine invertebrates in response to OA. These results suggest that oysters with prior larval exposure history to OA had the ability to trigger rapid local adaptive responses via epigenetic modification to cope with multiple stressors in the field.
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Affiliation(s)
- Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.,School of Applied Science, Temasek Polytechnic, Singapore, Singapore
| | - Yang Li
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,The Joint Laboratory for Marine Ecology and Environmental Sciences (JLMEES), Institute of Oceanology, Chinese Acadamy of Sciences, Beijing, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.,The Joint Laboratory for Marine Ecology and Environmental Sciences (JLMEES), The Swire Institute of Marine Sciences, The University of Hong Kong, Hong Kong SAR, China
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Gurr SJ, Trigg SA, Vadopalas B, Roberts SB, Putnam HM. Acclimatory gene expression of primed clams enhances robustness to elevated pCO 2. Mol Ecol 2022; 31:5005-5023. [PMID: 35947503 DOI: 10.1111/mec.16644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022]
Abstract
Sub-lethal exposure to environmental challenges may enhance ability to cope with chronic or repeated change, a process known as priming. In a previous study, pre-exposure to seawater enriched with pCO2 improved growth and reduced antioxidant capacity of juvenile Pacific geoduck Panopea generosa, suggesting that transcriptional shifts may drive phenotypic modifications post-priming. To this end, juvenile clams were sampled and TagSeq gene expression data analyzed after 1) a 110-day acclimation under ambient (921 μatm, naïve) and moderately-elevated pCO2 (2870 μatm, pre-exposed); then following 2) a second 7-day exposure to three pCO2 treatments (ambient: 754 μatm; moderately-elevated: 2750 μatm; severely-elevated: 4940 μatm), a 7-day return to ambient pCO2 , and a third 7-day exposure to two pCO2 treatments (ambient: 967 μatm; moderately-elevated: 3030 μatm). Pre-exposed geoducks frontloaded genes for stress and apoptosis/innate immune response, homeostatic processes, protein degradation, and transcriptional modifiers. Pre-exposed geoducks were also responsive to subsequent encounters, with gene sets enriched for mitochondrial recycling and immune defense under elevated pCO2 and energy metabolism and biosynthesis under ambient recovery. In contrast, gene sets with higher expression in naïve clams were enriched for fatty-acid degradation and glutathione components, suggesting naïve clams could be depleting endogenous fuels, with unsustainable energetic requirements if changes in carbonate chemistry persist. Collectively, our transcriptomic data indicates pCO2 priming during post-larval periods could, via gene expression regulation, enhance robustness in bivalves to environmental change. Such priming approaches may be beneficial for aquaculture, as seafood demand intensifies concurrent with increasing climate change in marine systems.
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Affiliation(s)
- Samuel J Gurr
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Shelly A Trigg
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, USA
| | | | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
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7
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Venkataraman YR, White SJ, Roberts SB. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics 2022; 23:556. [PMID: 35927609 PMCID: PMC9351233 DOI: 10.1186/s12864-022-08781-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/13/2022] [Indexed: 12/30/2022] Open
Abstract
Background There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08781-5.
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Affiliation(s)
- Yaamini R Venkataraman
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543, USA. .,School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA.
| | - Samuel J White
- School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
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8
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Lyketsos CG, Roberts SB, Swift EK, Quina A, Moon G, Kremer I, Tariot P, Fillit H, Bovenkamp DE, Zandi PP, Haaga JG. Standardizing Electronic Health Record Data on AD/ADRD to Accelerate Health Equity in Prevention, Detection, and Treatment. J Prev Alzheimers Dis 2022; 9:556-560. [PMID: 35841257 DOI: 10.14283/jpad.2022.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Improving the prevention, detection, and treatment of Alzheimer's disease and Alzheimer's disease related dementias (AD/ADRD) across racial, ethnic, and other diverse populations is a national priority. To this end, this paper proposes the development of the Standard Health Record for Dementia (SHRD, pronounced "shared") for collecting and sharing AD/ADRD real-world data (RWD). SHRD would replace the current unstandardized, fragmented, or missing state of key RWD with an open source, consensus-based, and interoperable common data standard. This paper describes how SHRD could leverage the best practices of the Minimal Common Oncology Data Elements (mCODETM) initiative to advance prevention, detection, and treatment; gain adoption by clinicians and electronic health record (EHR) vendors; and establish sustainable business and governance models. It describes a range of potential use cases to advance equity, including strengthening public health surveillance by facilitating AD/ADRD registry reporting; improving case detection and staging; and diversifying participation in clinical trials.
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Affiliation(s)
- C G Lyketsos
- Elaine K. Swift, PhD, The MITRE Corporation, McLean, VA, USA,
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9
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Trigg SA, Venkataraman YR, Gavery MR, Roberts SB, Bhattacharya D, Downey-Wall A, Eirin-Lopez JM, Johnson KM, Lotterhos KE, Puritz JB, Putnam HM. Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Mol Ecol Resour 2021; 22:1247-1261. [PMID: 34709728 DOI: 10.1111/1755-0998.13542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022]
Abstract
There is a growing focus on the role of DNA methylation in the ability of marine invertebrates to rapidly respond to changing environmental factors and anthropogenic impacts. However, genome-wide DNA methylation studies in nonmodel organisms are currently hampered by a limited understanding of methodological biases. Here, we compare three methods for quantifying DNA methylation at single base-pair resolution-whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and methyl-CpG binding domain bisulfite sequencing (MBDBS)-using multiple individuals from two reef-building coral species with contrasting environmental sensitivity. All methods reveal substantially greater methylation in Montipora capitata (11.4%) than the more sensitive Pocillopora acuta (2.9%). The majority of CpG methylation in both species occurs in gene bodies and flanking regions. In both species, MBDBS has the greatest capacity for detecting CpGs in coding regions at our sequencing depth, but MBDBS may be influenced by intrasample methylation heterogeneity. RRBS yields robust information for specific loci albeit without enrichment of any particular genome feature and with significantly reduced genome coverage. Relative genome size strongly influences the number and location of CpGs detected by each method when sequencing depth is limited, illuminating nuances in cross-species comparisons. As genome-wide methylation differences, supported by data across bisulfite sequencing methods, may contribute to environmental sensitivity phenotypes in critical marine invertebrate taxa, these data provide a genomic resource for investigating the functional role of DNA methylation in environmental tolerance.
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Affiliation(s)
- Shelly A Trigg
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Yaamini R Venkataraman
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Mackenzie R Gavery
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Alan Downey-Wall
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, North Miami, Florida, USA
| | - Kevin M Johnson
- Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, California, USA.,California Sea Grant, University of California San Diego, La Jolla, California, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA
| | - Jonathan B Puritz
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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10
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Chandra Rajan K, Meng Y, Yu Z, Roberts SB, Vengatesen T. Oyster biomineralization under ocean acidification: From genes to shell. Glob Chang Biol 2021; 27:3779-3797. [PMID: 33964098 DOI: 10.1111/gcb.15675] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/02/2021] [Indexed: 05/27/2023]
Abstract
Biomineralization is one of the key processes that is notably affected in marine calcifiers such as oysters under ocean acidification (OA). Understanding molecular changes in the biomineralization process under OA and its heritability, therefore, is key to developing conservation strategies for protecting ecologically and economically important oyster species. To do this, in this study, we have explicitly chosen the tissue involved in biomineralization (mantle) of an estuarine commercial oyster species, Crassostrea hongkongensis. The primary aim of this study is to understand the influence of DNA methylation over gene expression of mantle tissue under decreased ~pH 7.4, a proxy of OA, and to extrapolate if these molecular changes can be observed in the product of biomineralization-the shell. We grew early juvenile C. hongkongensis, under decreased ~pH 7.4 and control ~pH 8.0 over 4.5 months and studied OA-induced DNA methylation and gene expression patterns along with shell properties such as microstructure, crystal orientation and hardness. The population of oysters used in this study was found to be moderately resilient to OA at the end of the experiment. The expression of key biomineralization-related genes such as carbonic anhydrase and alkaline phosphatase remained unaffected; thus, the mechanical properties of the shell (shell growth rate, hardness and crystal orientation) were also maintained without any significant difference between control and OA conditions with signs of severe dissolution. In addition, this study makes three major conclusions: (1) higher expression of Ca2+ binding/signalling-related genes in the mantle plays a key role in maintaining biomineralization under OA; (2) DNA methylation changes occur in response to OA; however, these methylation changes do not directly control gene expression; and (3) OA would be more of a 'dissolution problem' rather than a 'biomineralization problem' for resilient species that maintain calcification rate with normal shell growth and mechanical properties.
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Affiliation(s)
- Kanmani Chandra Rajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Yuan Meng
- State Key Laboratory of Respiratory Disease, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ziniu Yu
- South China Sea Institute of Oceanology, Guangzhou, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Thiyagarajan Vengatesen
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
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11
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Gurr SJ, Wanamaker SA, Vadopalas B, Roberts SB, Putnam HM. Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam. J Exp Biol 2021; 224:269329. [PMID: 34027545 DOI: 10.1242/jeb.233932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 05/18/2021] [Indexed: 01/06/2023]
Abstract
Although low levels of thermal stress, irradiance and dietary restriction can have beneficial effects for many taxa, stress acclimation remains little studied in marine invertebrates, even though they are threatened by climate change stressors such as ocean acidification. To test the role of life-stage and stress-intensity dependence in eliciting enhanced tolerance under subsequent stress encounters, we initially conditioned pediveliger Pacific geoduck (Panopea generosa) larvae to ambient and moderately elevated PCO2 (920 µatm and 2800 µatm, respectively) for 110 days. Then, clams were exposed to ambient, moderate or severely elevated PCO2 (750, 2800 or 4900 µatm, respectively) for 7 days and, following 7 days in ambient conditions, a 7-day third exposure to ambient (970 µatm) or moderate PCO2 (3000 µatm). Initial conditioning to moderate PCO2 stress followed by second and third exposure to severe and moderate PCO2 stress increased respiration rate, organic biomass and shell size, suggesting a stress-intensity-dependent effect on energetics. Additionally, stress-acclimated clams had lower antioxidant capacity compared with clams under ambient conditions, supporting the hypothesis that stress over postlarval-to-juvenile development affects oxidative status later in life. Time series and stress intensity-specific approaches can reveal life-stages and magnitudes of exposure, respectively, that may elicit beneficial phenotypic variation.
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Affiliation(s)
- Samuel J Gurr
- University of Rhode Island, College of the Environment and Life Sciences, 120 Flagg Rd, Kingston, RI 02881, USA
| | - Shelly A Wanamaker
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St, Seattle, WA 98105, USA
| | - Brent Vadopalas
- University of Washington, Washington Sea Grant, 3716 Brooklyn Ave NE, Seattle, WA 98105, USA
| | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St, Seattle, WA 98105, USA
| | - Hollie M Putnam
- University of Rhode Island, College of the Environment and Life Sciences, 120 Flagg Rd, Kingston, RI 02881, USA
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Dimond JL, Nguyen N, Roberts SB. DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING. G3 (Bethesda) 2021; 11:6275752. [PMID: 33989381 PMCID: PMC8496274 DOI: 10.1093/g3journal/jkab148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/15/2021] [Indexed: 11/20/2022]
Abstract
Symbiosis with protists is common among cnidarians such as corals and sea anemones and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species.
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Affiliation(s)
- James L Dimond
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98195 USA.,Western Washington University, Shannon Point Marine Center, 1900 Shannon Point Rd., Anacortes, WA 98221 USA
| | - Nhung Nguyen
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY 14456 USA.,South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98195 USA
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Timmins-Schiffman E, White SJ, Thompson RE, Vadopalas B, Eudeline B, Nunn BL, Roberts SB. Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery. Environ Microbiome 2021; 16:7. [PMID: 33902744 PMCID: PMC8066469 DOI: 10.1186/s40793-021-00376-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Microbial communities are ubiquitous throughout ecosystems and are commensal with hosts across taxonomic boundaries. Environmental and species-specific microbiomes are instrumental in maintaining ecosystem and host health, respectively. The introduction of pathogenic microbes that shift microbiome community structure can lead to illness and death. Understanding the dynamics of microbiomes across a diversity of environments and hosts will help us to better understand which taxa forecast survival and which forecast mortality events. RESULTS We characterized the bacterial community microbiome in the water of a commercial shellfish hatchery in Washington state, USA, where the hatchery has been plagued by recurring and unexplained larval mortality events. By applying the complementary methods of metagenomics and metaproteomics we were able to more fully characterize the bacterial taxa in the hatchery at high (pH 8.2) and low (pH 7.1) pH that were metabolically active versus present but not contributing metabolically. There were shifts in the taxonomy and functional profile of the microbiome between pH and over time. Based on detected metagenomic reads and metaproteomic peptide spectral matches, some taxa were more metabolically active than expected based on presence alone (Deltaproteobacteria, Alphaproteobacteria) and some were less metabolically active than expected (e.g., Betaproteobacteria, Cytophagia). There was little correlation between potential and realized metabolic function based on Gene Ontology analysis of detected genes and peptides. CONCLUSION The complementary methods of metagenomics and metaproteomics contribute to a more full characterization of bacterial taxa that are potentially active versus truly metabolically active and thus impact water quality and inter-trophic relationships.
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Affiliation(s)
- Emma Timmins-Schiffman
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195 USA
| | - Samuel J. White
- School of Aquatic and Fishery Sciences, University of Washington, 1122 Boat St., Seattle, WA 98195 USA
| | - Rhonda Elliott Thompson
- Taylor Shellfish Hatchery, 701 Broadspit Rd., Quilcene, WA 98376 USA
- Mason County Public Health, 415 N 6th St., Shelton, WA 98584 USA
| | - Brent Vadopalas
- Washington Sea Grant, University of Washington, 3716 Brooklyn Ave NE, Seattle, WA 98105 USA
| | - Benoit Eudeline
- Taylor Shellfish Hatchery, 701 Broadspit Rd., Quilcene, WA 98376 USA
| | - Brook L. Nunn
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195 USA
| | - Steven B. Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122 Boat St., Seattle, WA 98195 USA
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Lim YK, Cheung K, Dang X, Roberts SB, Wang X, Thiyagarajan V. DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis. Mar Environ Res 2021; 163:105217. [PMID: 33276167 DOI: 10.1016/j.marenvres.2020.105217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/07/2020] [Accepted: 05/10/2020] [Indexed: 06/12/2023]
Abstract
Unprecedented rate of increased CO2 level in the ocean and the subsequent changes in carbonate system including decreased pH, known as ocean acidification (OA), is predicted to disrupt not only the calcification process but also several other physiological and developmental processes in a variety of marine organisms, including edible oysters. Nonetheless, not all species are vulnerable to those OA threats, e.g. some species may be able to cope with OA stress using environmentally induced modifications on gene and protein expressions. For example, external environmental stressors including OA can influence the addition and removal of methyl groups through epigenetic modification (e.g. DNA methylation) process to turn gene expression "on or off" as part of a rapid adaptive mechanism to cope with OA. In this study, we tested the above hypothesis through testing the effect of OA, using decreased pH 7.4 as proxy, on DNA methylation pattern of an endemic and a commercially important estuary oyster species, Crassostrea hongkongensis at the time of larval habitat selection and metamorphosis. Larval growth rate did not differ between control pH 8.1 and treatment pH 7.4. The metamorphosis rate of the pediveliger larvae was higher at pH 7.4 than those in control pH 8.1, however over one-third of the larvae raised at pH 7.4 failed to attach on optimal substrate as defined by biofilm presence. During larval development, a total of 130 genes were differentially methylated across the two treatments. The differential methylation in the larval genes may have partially accounted for the higher metamorphosis success rate under decreased pH 7.4 but with poor substratum selection ability. Differentially methylated loci were concentrated in the exon regions and appear to be associated with cytoskeletal and signal transduction, oxidative stress, metabolic processes, and larval metamorphosis, which implies the high potential of C. hongkongensis larvae to acclimate and adapt through non-genetic ways to OA threats within a single generation.
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Affiliation(s)
- Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Khan Cheung
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122, NE Boat Street, Seattle, WA, USA
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
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Lim YK, Cheung K, Dang X, Roberts SB, Wang X, Thiyagarajan V. DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis. Mar Environ Res 2021; 163:105214. [PMID: 33221553 DOI: 10.1016/j.marenvres.2020.105214] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Unprecedented rate of increased CO2 level in the ocean and the subsequent changes in carbonate system including decreased pH, known as ocean acidification (OA), is predicted to disrupt not only the calcification process but also several other physiological and developmental processes in a variety of marine organisms, including edible oysters. Nonetheless, not all species are vulnerable to those OA threats, e.g. some species may be able to cope with OA stress using environmentally induced modifications on gene and protein expressions. For example, external environmental stressors including OA can influence the addition and removal of methyl groups through epigenetic modification (e.g. DNA methylation) process to turn gene expression "on or off" as part of a rapid adaptive mechanism to cope with OA. In this study, we tested the above hypothesis through testing the effect of OA, using decreased pH 7.4 as proxy, on DNA methylation pattern of an endemic and a commercially important estuary oyster species, Crassostrea hongkongensis at the time of larval habitat selection and metamorphosis. Larval growth rate did not differ between control pH 8.1 and treatment pH 7.4. The metamorphosis rate of the pediveliger larvae was higher at pH 7.4 than those in control pH 8.1, however over one-third of the larvae raised at pH 7.4 failed to attach on optimal substrate as defined by biofilm presence. During larval development, a total of 130 genes were differentially methylated across the two treatments. The differential methylation in the larval genes may have partially accounted for the higher metamorphosis success rate under decreased pH 7.4 but with poor substratum selection ability. Differentially methylated loci were concentrated in the exon regions and appear to be associated with cytoskeletal and signal transduction, oxidative stress, metabolic processes, and larval metamorphosis, which implies the high potential of C. hongkongensis larvae to acclimate and adapt through non-genetic ways to OA threats within a single generation.
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Affiliation(s)
- Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Khan Cheung
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, WA, USA
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China.
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Timmins-Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB. Larval Geoduck (Panopea generosa) Proteomic Response to Ciliates. Sci Rep 2020; 10:6042. [PMID: 32269285 PMCID: PMC7142153 DOI: 10.1038/s41598-020-63218-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/31/2020] [Indexed: 11/21/2022] Open
Abstract
The innate immune response is active in invertebrate larvae from early development. Induction of immune response pathways may occur as part of the natural progression of larval development, but an up-regulation of pathways can also occur in response to a pathogen. Here, we took advantage of a protozoan ciliate infestation of a larval geoduck clam culture in a commercial hatchery to investigate the molecular underpinnings of the innate immune response of the larvae to the pathogen. Larval proteomes were analyzed on days 4-10 post-fertilization; ciliates were present on days 8 and 10 post-fertilization. Through comparisons with larval cultures that did not encounter ciliates, proteins implicated in the response to ciliate presence were identified using mass spectrometry-based proteomics. Ciliate response proteins included many associated with ribosomal synthesis and protein translation, suggesting the importance of protein synthesis during the larval immune response. There was also an increased abundance of proteins typically associated with the stress and immune responses during ciliate exposure, such as heat shock proteins, glutathione metabolism, and the reactive oxygen species response. These findings provide a basic understanding of the bivalve molecular response to a mortality-inducing ciliate and improved characterization of the ontogenetic development of the innate immune response.
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Affiliation(s)
- Emma Timmins-Schiffman
- University of Washington, Department of Genome Sciences, 3720 15th Ave NE, Seattle, WA, 98195, United States
| | - José M Guzmán
- University of Washington, School of Aquatic and Fishery Sciences, 1122 Boat St., Seattle, WA, 98195, United States
| | - Rhonda Elliott Thompson
- Taylor Shellfish Hatchery, 701 Broadspit Rd., Quilcene, WA, 98376, United States
- Mason County Public Health, 415N 6th St., Shelton, WA, 98584, United States
| | - Brent Vadopalas
- University of Washington, School of Aquatic and Fishery Sciences, 1122 Boat St., Seattle, WA, 98195, United States
| | - Benoit Eudeline
- Taylor Shellfish Hatchery, 701 Broadspit Rd., Quilcene, WA, 98376, United States
| | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, 1122 Boat St., Seattle, WA, 98195, United States.
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Gurr SJ, Vadopalas B, Roberts SB, Putnam HM. Metabolic recovery and compensatory shell growth of juvenile Pacific geoduck Panopea generosa following short-term exposure to acidified seawater. Conserv Physiol 2020; 8:coaa024. [PMID: 32274068 PMCID: PMC7125045 DOI: 10.1093/conphys/coaa024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/12/2019] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
While acute stressors can be detrimental, environmental stress conditioning can improve performance. To test the hypothesis that physiological status is altered by stress conditioning, we subjected juvenile Pacific geoduck, Panopea generosa, to repeated exposures of elevated pCO2 in a commercial hatchery setting followed by a period in ambient common garden. Respiration rate and shell length were measured for juvenile geoduck periodically throughout short-term repeated reciprocal exposure periods in ambient (~550 μatm) or elevated (~2400 μatm) pCO2 treatments and in common, ambient conditions, 5 months after exposure. Short-term exposure periods comprised an initial 10-day exposure followed by 14 days in ambient before a secondary 6-day reciprocal exposure. The initial exposure to elevated pCO2 significantly reduced respiration rate by 25% relative to ambient conditions, but no effect on shell growth was detected. Following 14 days in common garden, ambient conditions, reciprocal exposure to elevated or ambient pCO2 did not alter juvenile respiration rates, indicating ability for metabolic recovery under subsequent conditions. Shell growth was negatively affected during the reciprocal treatment in both exposure histories; however, clams exposed to the initial elevated pCO2 showed compensatory growth with 5.8% greater shell length (on average between the two secondary exposures) after 5 months in ambient conditions. Additionally, clams exposed to the secondary elevated pCO2 showed 52.4% increase in respiration rate after 5 months in ambient conditions. Early exposure to low pH appears to trigger carryover effects suggesting bioenergetic re-allocation facilitates growth compensation. Life stage-specific exposures to stress can determine when it may be especially detrimental, or advantageous, to apply stress conditioning for commercial production of this long-lived burrowing clam.
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Affiliation(s)
- Samuel J Gurr
- College of the Environment and Life Sciences, University of Rhode Island, 120 Flagg Rd, Kingston, RI 02881, USA
| | - Brent Vadopalas
- Washington Sea Grant, University of Washington, 3716 Brooklyn Ave NE, Seattle, WA 98105, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA 98105, USA
| | - Hollie M Putnam
- College of the Environment and Life Sciences, University of Rhode Island, 120 Flagg Rd, Kingston, RI 02881, USA
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Spencer LH, Venkataraman YR, Crim R, Ryan S, Horwith MJ, Roberts SB. Carryover effects of temperature and pCO 2 across multiple Olympia oyster populations. Ecol Appl 2020; 30:e02060. [PMID: 31863716 DOI: 10.1002/eap.2060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/07/2019] [Accepted: 10/21/2019] [Indexed: 05/20/2023]
Abstract
Predicting how populations will respond to ocean change across generations is critical to effective conservation of marine species. One emerging factor is the influence of parental exposures on offspring phenotype, known as intergenerational carryover effects. Parental exposure may deliver beneficial or detrimental characteristics to offspring that can influence larval recruitment patterns, thus shaping how populations and community structure respond to ocean change. Impacts of adult exposure to elevated winter temperature and pCO2 on reproduction and offspring viability were examined in the Olympia oyster (Ostrea lurida) using three populations of adult, hatchery-reared O. lurida, plus an additional cohort spawned from one of the populations. Oysters were sequentially exposed to elevated temperature (+4°C, at 10°C), followed by elevated pCO2 (+2,204 μatm, at 3,045 μatm) during winter months. Male gametes were more developed after elevated temperature exposure and less developed after high pCO2 exposure, but there was no impact on female gametes or sex ratios. Oysters previously exposed to elevated winter temperature released larvae earlier, regardless of pCO2 exposure. Those exposed to elevated winter temperature as a sole treatment released more larvae on a daily basis but, when also exposed to high pCO2 , there was no effect. These combined results indicate that elevated winter temperature accelerates O. lurida spermatogenesis, resulting in earlier larval release and increased production, with elevated pCO2 exposure negating effects of elevated temperature. Altered recruitment patterns may therefore follow warmer winters due to precocious spawning, but these effects may be masked by coincidental high pCO2 . Offspring were reared in common conditions for 1 yr, then deployed for 3 months in four estuarine bays with distinct environmental conditions. Offspring of parents exposed to elevated pCO2 had higher survival rates in two of the four bays. This carryover effect demonstrates that parental conditions can have substantial ecologically relevant impacts that should be considered when predicting impacts of environmental change. Furthermore, Olympia oysters may be more resilient in certain environments when progenitors are pre-conditioned in stressful conditions. Combined with other recent studies, our work suggests that the Olympia may be more equipped than other oysters for the challenge of a changing ocean.
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Affiliation(s)
- Laura H Spencer
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, Washington, 98105, USA
| | - Yaamini R Venkataraman
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, Washington, 98105, USA
| | - Ryan Crim
- Puget Sound Restoration Fund, 8001 NE Day Road West, Bainbridge Island, Washington, 98110, USA
| | - Stuart Ryan
- Puget Sound Restoration Fund, 8001 NE Day Road West, Bainbridge Island, Washington, 98110, USA
| | - Micah J Horwith
- Washington State Department of Natural Resources, 1111 Washington Street SE, MS 47027, Olympia, Washington, 98504, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, Washington, 98105, USA
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Timmins‐Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB. Dynamic response in the larval geoduck ( Panopea generosa) proteome to elevated pCO 2. Ecol Evol 2020; 10:185-197. [PMID: 31988722 PMCID: PMC6972802 DOI: 10.1002/ece3.5885] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/15/2019] [Accepted: 11/10/2019] [Indexed: 12/20/2022] Open
Abstract
Pacific geoducks (Panopea generosa) are clams found along the northeast Pacific coast where they are important components of coastal and estuarine ecosystems and a major aquaculture product. The Pacific coastline, however, is also experiencing rapidly changing ocean habitat, including significant reductions in pH. To better understand the physiological impact of ocean acidification on geoduck clams, we characterized for the first time the proteomic profile of this bivalve during larval development and compared it to that of larvae exposed to low pH conditions. Geoduck larvae were reared at pH 7.5 (ambient) or pH 7.1 in a commercial shellfish hatchery from day 6 to day 19 postfertilization and sampled at six time points for an in-depth proteomics analysis using high-resolution data-dependent analysis. Larvae reared at low pH were smaller than those reared at ambient pH, especially in the prodissoconch II phase of development, and displayed a delay in their competency for settlement. Proteomic profiles revealed that metabolic, cell cycle, and protein turnover pathways differed between the two pH and suggested that differing phenotypic outcomes between pH 7.5 and 7.1 are likely due to environmental disruptions to the timing of physiological events. In summary, ocean acidification results in elevated energetic demand on geoduck larvae, resulting in delayed development and disruptions to normal molecular developmental pathways, such as carbohydrate metabolism, cell growth, and protein synthesis.
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Affiliation(s)
| | - José M. Guzmán
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Rhonda Elliott Thompson
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
- Taylor Shellfish HatcheryQuilceneWAUSA
- Mason County Public HealthSheltonWAUSA
| | | | | | - Steven B. Roberts
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
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Spencer LH, Horwith M, Lowe AT, Venkataraman YR, Timmins-Schiffman E, Nunn BL, Roberts SB. Pacific geoduck (Panopea generosa) resilience to natural pH variation. Comp Biochem Physiol Part D Genomics Proteomics 2019; 30:91-101. [PMID: 30818101 DOI: 10.1016/j.cbd.2019.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 02/02/2023]
Abstract
Pacific geoduck aquaculture is a growing industry, however, little is known about how geoduck respond to varying environmental conditions, or how the industry will fare under projected climate conditions. To understand how geoduck production may be impacted by low pH associated with ocean acidification, multi-faceted environmental heterogeneity needs to be included to understand species and community responses. In this study, eelgrass habitats and environmental heterogeneity across four estuarine bays were leveraged to examine low pH effects on geoduck under different natural regimes, using targeted proteomics to assess physiology. Juvenile geoduck were deployed in eelgrass and adjacent unvegetated habitats for 30 days while pH, temperature, dissolved oxygen, and salinity were monitored. Across the four bays, pH was lower in unvegetated habitats compared to eelgrass habitats. However this did not impact geoduck growth, survival, or proteomic abundance patterns in gill tissue. Temperature and dissolved oxygen differences across all locations corresponded to differences in growth and targeted protein abundance patterns. Specifically, three protein abundance levels (trifunctional-enzyme β-subunit, puromycin-sensitive aminopeptidase, and heat shock protein 90-α) and shell growth positively correlated with dissolved oxygen variability and inversely correlated with mean temperature. These results demonstrate that geoduck may be resilient to low pH in a natural setting, but other abiotic factors (i.e. temperature, dissolved oxygen variability) may have a greater influence on geoduck physiology. In addition this study contributes to the understanding of how eelgrass patches influences water chemistry.
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Affiliation(s)
- Laura H Spencer
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St, Seattle, WA 98105, United States
| | - Micah Horwith
- Washington State Department of Natural Resources, 1111 Washington St SE, MS 47027, Olympia, WA 98504, United States
| | - Alexander T Lowe
- University of Washington, Biological Sciences, 24 Kincaid Hall, Seattle, WA 98105, United States
| | - Yaamini R Venkataraman
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St, Seattle, WA 98105, United States
| | - Emma Timmins-Schiffman
- University of Washington, Genome Sciences, William H. Foege Hall, 3720 15th Ave NE, Seattle, WA 98195, United States
| | - Brook L Nunn
- University of Washington, Genome Sciences, William H. Foege Hall, 3720 15th Ave NE, Seattle, WA 98195, United States
| | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St, Seattle, WA 98105, United States.
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Rodriguez‐Casariego JA, Ladd MC, Shantz AA, Lopes C, Cheema MS, Kim B, Roberts SB, Fourqurean JW, Ausio J, Burkepile DE, Eirin‐Lopez JM. Coral epigenetic responses to nutrient stress: Histone H2A.X phosphorylation dynamics and DNA methylation in the staghorn coral Acropora cervicornis. Ecol Evol 2018; 8:12193-12207. [PMID: 30598811 PMCID: PMC6303763 DOI: 10.1002/ece3.4678] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/28/2018] [Accepted: 10/05/2018] [Indexed: 12/19/2022] Open
Abstract
Nutrient pollution and thermal stress constitute two of the main drivers of global change in the coastal oceans. While different studies have addressed the physiological effects and ecological consequences of these stressors in corals, the role of acquired modifications in the coral epigenome during acclimatory and adaptive responses remains unknown. The present work aims to address that gap by monitoring two types of epigenetic mechanisms, namely histone modifications and DNA methylation, during a 7-week-long experiment in which staghorn coral fragments (Acropora cervicornis) were exposed to nutrient stress (nitrogen, nitrogen + phosphorus) in the presence of thermal stress. The major conclusion of this experiment can be summarized by two main results: First, coral holobiont responses to the combined effects of nutrient enrichment and thermal stress involve the post-translational phosphorylation of the histone variant H2A.X (involved in responses to DNA damage), as well as nonsignificant modifications in DNA methylation trends. Second, the reduction in H2A.X phosphorylation (and the subsequent potential impairment of DNA repair mechanisms) observed after prolonged coral exposure to nitrogen enrichment and thermal stress is consistent with the symbiont-driven phosphorus limitation previously observed in corals subject to nitrogen enrichment. The alteration of this epigenetic mechanism could help to explain the synergistic effects of nutrient imbalance and thermal stress on coral fitness (i.e., increased bleaching and mortality) while supporting the positive effect of phosphorus addition to improving coral resilience to thermal stress. Overall, this work provides new insights into the role of epigenetic mechanisms during coral responses to global change, discussing future research directions and the potential benefits for improving restoration, management and conservation of coral reef ecosystems worldwide.
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Affiliation(s)
- Javier A. Rodriguez‐Casariego
- Environmental Epigenetics Laboratory, Institute of Water and Environment, Department of Biological SciencesFlorida International UniversityMiamiFlorida
| | - Mark C. Ladd
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
| | - Andrew A. Shantz
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
| | - Christian Lopes
- Seagrass Laboratory, Institute of Water and Environment, Department of Biological SciencesFlorida International UniversityMiamiFlorida
| | - Manjinder S. Cheema
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Bohyun Kim
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Steven B. Roberts
- School of Aquatic and Fishery ScienceUniversity of WashingtonSeattleWashington
| | - James W. Fourqurean
- Seagrass Laboratory, Institute of Water and Environment, Department of Biological SciencesFlorida International UniversityMiamiFlorida
| | - Juan Ausio
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Deron E. Burkepile
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
| | - Jose M. Eirin‐Lopez
- Environmental Epigenetics Laboratory, Institute of Water and Environment, Department of Biological SciencesFlorida International UniversityMiamiFlorida
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Silliman KE, Bowyer TK, Roberts SB. Consistent differences in fitness traits across multiple generations of Olympia oysters. Sci Rep 2018; 8:6080. [PMID: 29666427 PMCID: PMC5904129 DOI: 10.1038/s41598-018-24455-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/28/2018] [Indexed: 12/04/2022] Open
Abstract
Adaptive evolution and plasticity are two mechanisms that facilitate phenotypic differences between populations living in different environments. Understanding which mechanism underlies variation in fitness-related traits is a crucial step in designing conservation and restoration management strategies for taxa at risk from anthropogenic stressors. Olympia oysters (Ostrea lurida) have received considerable attention with regard to restoration, however there is limited information on adaptive population structure. Using oysters raised under common conditions for up to two generations (F1s and F2s), we tested for evidence of divergence in reproduction, larval growth, and juvenile growth among three populations in Puget Sound, Washington. We found that the population with the fastest growth rate also exhibited delayed and reduced reproductive activity, indicating a potential adaptive trade-off. Our results corroborate and extend upon a previous reciprocal transplant study on F1 oysters from the same populations, indicating that variation in growth rate and differences in reproductive timing are consistent across both natural and laboratory environments and have a strongly heritable component that cannot be entirely attributed to plasticity.
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Affiliation(s)
| | - Tynan K Bowyer
- University of Chicago, Ecology and Evolution, Chicago, 60637, United States
| | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, 98195, United States
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Heare JE, White SJ, Vadopalas B, Roberts SB. Differential response to stress in Ostrea lurida as measured by gene expression. PeerJ 2018; 6:e4261. [PMID: 29362695 PMCID: PMC5772385 DOI: 10.7717/peerj.4261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/22/2017] [Indexed: 11/20/2022] Open
Abstract
Olympia oysters are the only oyster native to the west coast of North America. The population within Puget Sound, WA has been decreasing significantly since the early 1900’s. Current restoration efforts are focused on supplementing local populations with hatchery bred oysters. A recent study by Heare et al. (2017) has shown differences in stress response in oysters from different locations in Puget Sound however, nothing is known about the underlying mechanisms associated with these observed differences. In this study, expression of genes associated with growth, immune function, and gene regulatory activity in oysters from Oyster Bay, Dabob Bay, and Fidalgo Bay were characterized following temperature and mechanical stress. We found that heat stress and mechanical stress significantly changed expression in molecular regulatory activity and immune response, respectively. We also found that oysters from Oyster Bay had the most dramatic response to stress at the gene expression level. These data provide important baseline information on the physiological response of Ostrea lurida to stress and provide clues to underlying performance differences in the three populations examined.
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Affiliation(s)
- J Emerson Heare
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
| | - Samuel J White
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
| | - Brent Vadopalas
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
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Abstract
Epigenetics has attracted considerable attention with respect to its potential value in many areas of agricultural production, particularly under conditions where the environment can be manipulated or natural variation exists. Here we introduce key concepts and definitions of epigenetic mechanisms, including DNA methylation, histone modifications and non-coding RNA, review the current understanding of epigenetics in both fish and shellfish, and propose key areas of aquaculture where epigenetics could be applied. The first key area is environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either within or between generations to produce a desired phenotype. The second key area is epigenetic selection, which, alone or combined with genetic selection, may increase the reliability of producing animals with desired phenotypes. Based on aspects of life history and husbandry practices in aquaculture species, the application of epigenetic knowledge could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend traditional assumptions about selection practices. Ultimately, there are still many unanswered questions regarding how epigenetic mechanisms might be leveraged in aquaculture.
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Affiliation(s)
- Mackenzie R Gavery
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
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White SJ, Vadopalas B, Silliman K, Roberts SB. Genotoype-by-sequencing of three geographically distinct populations of Olympia oysters, Ostrea lurida. Sci Data 2017; 4:170130. [PMID: 28895940 PMCID: PMC5595046 DOI: 10.1038/sdata.2017.130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/28/2017] [Indexed: 11/23/2022] Open
Abstract
Olympia oysters are found along the west coast of North America and as the only native oyster species in the region, receive considerable attention with regard to restoration and conservation. Knowledge of genetic structure of this species is essential for resource managers. Here we provide genetic data for three distinct populations of Olympia oysters in Puget Sound, Washington, USA in the form of genotype-by-sequencing data (GBS). Specifically, this includes description of sequence data and a derived table that provides single nucleotide polymorphism (SNP) information for 10,363 loci. These data are valuable not only for resource managers responsible for restoration aquaculture practices, but can provide insight into ecological drivers of selection and diversity.
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Affiliation(s)
- Samuel J White
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, Washington 98105, USA
| | - Brent Vadopalas
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, Washington 98105, USA
| | - Katherine Silliman
- University of Chicago, Committee on Evolutionary Biology, Chicago, Illinois 60637, USA
| | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, Washington 98105, USA
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Dimond JL, Gamblewood SK, Roberts SB. Genetic and epigenetic insight into morphospecies in a reef coral. Mol Ecol 2017; 26:5031-5042. [DOI: 10.1111/mec.14252] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 12/27/2022]
Affiliation(s)
- James L. Dimond
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
- Shannon Point Marine Center Western Washington University Anacortes WA USA
| | | | - Steven B. Roberts
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
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27
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Timmins-Schiffman EB, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SB. Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation. J Proteome Res 2017; 16:3298-3309. [PMID: 28730805 DOI: 10.1021/acs.jproteome.7b00288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Geoduck clams (Panopea generosa) are an increasingly important fishery and aquaculture product along the eastern Pacific coast from Baja California, Mexico, to Alaska. These long-lived clams are highly fecund, although sustainable hatchery production of genetically diverse larvae is hindered by the lack of sexual dimorphism, resulting in asynchronous spawning of broodstock, unequal sex ratios, and low numbers of breeders. The development of assays of gonad physiology could indicate sex and maturation stage as well as be used to assess the status of natural populations. Proteomic profiles were determined for three reproductive maturation stages in both male and female clams using data-dependent acquisition (DDA) of gonad proteins. Gonad proteomes became increasingly divergent between males and females as maturation progressed. The DDA data were used to develop targets analyzed with selected reaction monitoring (SRM) in gonad tissue as well as hemolymph. The SRM assay yielded a suite of indicator peptides that can be used as an efficient assay to determine geoduck gonad maturation status. Application of SRM in hemolymph samples demonstrates that this procedure could effectively be used to assess reproductive status in marine mollusks in a nonlethal manner.
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Affiliation(s)
- Emma B Timmins-Schiffman
- Department of Genome Sciences, University of Washington , Seattle, Washington 98105, United States
| | - Grace A Crandall
- School of Aquatic and Fishery Sciences, University of Washington , Seattle, Washington 98105, United States
| | - Brent Vadopalas
- School of Aquatic and Fishery Sciences, University of Washington , Seattle, Washington 98105, United States
| | - Michael E Riffle
- Department of Biochemistry, University of Washington , Seattle, Washington 98105, United States
| | - Brook L Nunn
- Department of Genome Sciences, University of Washington , Seattle, Washington 98105, United States
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington , Seattle, Washington 98105, United States
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Roberts SB, Dryden R, Tsirikos AI. Thoracolumbar kyphosis in patients with mucopolysaccharidoses: clinical outcomes and predictive radiographic factors for progression of deformity. Bone Joint J 2016; 98-B:229-37. [PMID: 26850429 DOI: 10.1302/0301-620x.98b2.36144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AIMS Clinical and radiological data were reviewed for all patients with mucopolysaccharidoses (MPS) with thoracolumbar kyphosis managed non-operatively or operatively in our institution. METHODS In all 16 patients were included (eight female: eight male; 50% male), of whom nine had Hurler, five Morquio and two Hunter syndrome. Six patients were treated non-operatively (mean age at presentation of 6.3 years; 0.4 to 12.9); mean kyphotic progression +1.5(o)/year; mean follow-up of 3.1 years (1 to 5.1) and ten patients operatively (mean age at presentation of 4.7 years; 0.9 to 14.4); mean kyphotic progression 10.8(o)/year; mean follow-up of 8.2 years; 4.8 to 11.8) by circumferential arthrodesis with posterior instrumentation in patients with flexible deformities (n = 6). RESULTS In the surgical group (mean age at surgery of 6.6 years; 2.4 to 16.8); mean post-operative follow-up of 6.3 years (3.5 to 10.3), mean pre-operative thoracolumbar kyphosis of 74.3(o) (42(o) to 110(o)) was corrected to mean of 28.6(o) (0(o) to 65(o)) post-operatively, relating to a mean deformity correction of 66.9% (31% to 100%). Surgical complications included a deep wound infection treated by early debridement, apical non-union treated by posterior re-grafting, and stable adjacent segment spondylolisthesis managed non-operatively. Thoracolumbar kyphosis > +38(o) at initial presentation was identified as predicting progressively severe deformity with 90% sensitivity and 83% specificity. DISCUSSION This study demonstrates that severe thoracolumbar kyphosis in patients with MPS can be effectively treated by circumferential arthrodesis. Severity of kyphosis at initial presentation may predict progression of thoracolumbar deformity. Patients with MPS may be particularly susceptible to post-operative complications due to the underlying connective tissue disorder and inherent immunological compromise. TAKE HOME MESSAGE Clinical and radiological data were reviewed for all patients with mucopolysaccharidoses with thoracolumbar kyphosis managed non-operatively or operatively in our institution.
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Affiliation(s)
- S B Roberts
- Royal Hospital for Sick Children, Sciennes Road, Edinburgh, EH9 1LF, UK
| | - R Dryden
- Royal Hospital for Sick Children, Sciennes Road, Edinburgh, EH9 1LF, UK
| | - A I Tsirikos
- Scottish National Spine Deformity Centre, Royal Hospital for Sick Children, Sciennes Road, Edinburgh, EH9 1LF, UK
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Dimond JL, Roberts SB. Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change. Mol Ecol 2016; 25:1895-904. [DOI: 10.1111/mec.13414] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/26/2015] [Accepted: 10/01/2015] [Indexed: 12/27/2022]
Affiliation(s)
- James L. Dimond
- School of Aquatic and Fishery Sciences; University of Washington; 1122 Boat Street Seattle WA 98105 USA
| | - Steven B. Roberts
- School of Aquatic and Fishery Sciences; University of Washington; 1122 Boat Street Seattle WA 98105 USA
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Froehlich HE, Roberts SB, Essington TE. Evaluating hypoxia-inducible factor-1α mRNA expression in a pelagic fish, Pacific herring Clupea pallasii, as a biomarker for hypoxia exposure. Comp Biochem Physiol A Mol Integr Physiol 2015; 189:58-66. [DOI: 10.1016/j.cbpa.2015.07.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/28/2015] [Accepted: 07/28/2015] [Indexed: 11/29/2022]
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Fuess LE, Eisenlord ME, Closek CJ, Tracy AM, Mauntz R, Gignoux-Wolfsohn S, Moritsch MM, Yoshioka R, Burge CA, Harvell CD, Friedman CS, Hewson I, Hershberger PK, Roberts SB. Up in Arms: Immune and Nervous System Response to Sea Star Wasting Disease. PLoS One 2015; 10:e0133053. [PMID: 26176852 PMCID: PMC4503460 DOI: 10.1371/journal.pone.0133053] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/22/2015] [Indexed: 12/20/2022] Open
Abstract
Echinoderms, positioned taxonomically at the base of deuterostomes, provide an important system for the study of the evolution of the immune system. However, there is little known about the cellular components and genes associated with echinoderm immunity. The 2013-2014 sea star wasting disease outbreak is an emergent, rapidly spreading disease, which has led to large population declines of asteroids in the North American Pacific. While evidence suggests that the signs of this disease, twisting arms and lesions, may be attributed to a viral infection, the host response to infection is still poorly understood. In order to examine transcriptional responses of the sea star Pycnopodia helianthoides to sea star wasting disease, we injected a viral sized fraction (0.2 μm) homogenate prepared from symptomatic P. helianthoides into apparently healthy stars. Nine days following injection, when all stars were displaying signs of the disease, specimens were sacrificed and coelomocytes were extracted for RNA-seq analyses. A number of immune genes, including those involved in Toll signaling pathways, complement cascade, melanization response, and arachidonic acid metabolism, were differentially expressed. Furthermore, genes involved in nervous system processes and tissue remodeling were also differentially expressed, pointing to transcriptional changes underlying the signs of sea star wasting disease. The genomic resources presented here not only increase understanding of host response to sea star wasting disease, but also provide greater insight into the mechanisms underlying immune function in echinoderms.
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Affiliation(s)
- Lauren E. Fuess
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Morgan E. Eisenlord
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Collin J. Closek
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Allison M. Tracy
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Ruth Mauntz
- Donald P. Shiley Bioscience Center, San Diego, California, United States of America
| | - Sarah Gignoux-Wolfsohn
- Marine Science Center, Northeastern University, Nahant, Massachusetts, United States of America
| | - Monica M. Moritsch
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, United States of America
| | - Reyn Yoshioka
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Colleen A. Burge
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - C. Drew Harvell
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Carolyn S. Friedman
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Paul K. Hershberger
- U. S. Geological Survey, Western Fisheries Research Center, Marrowstone Marine Field Station, Nordland, Washington, United States of America
| | - Steven B. Roberts
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, United States of America
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Roberts SB, Wootton E, De Ferrari L, Albagha OM, Salter DM. Epigenetics of osteoarticular diseases: recent developments. Rheumatol Int 2015; 35:1293-305. [PMID: 25812537 DOI: 10.1007/s00296-015-3260-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/20/2015] [Indexed: 01/08/2023]
Abstract
A variety of osteoarticular conditions possess an underlying genetic aetiology. Large-scale genome-wide association studies have identified several genetic loci associated with osteoarticular conditions, but were unable to fully account for their estimated heritability. Epigenetic modifications including DNA methylation, histone modification, nucleosome positioning, and microRNA expression may help account for this incomplete heritability. This articles reviews insights from epigenetic studies in osteoarticular diseases, focusing on osteoarthritis, but also examines recent advances in rheumatoid arthritis, osteoporosis, systemic lupus erythematosus (SLE), ankylosing spondylitis, and sarcoma. Genome-wide methylation studies are permitting identification of novel candidate genes and molecular pathways, and the pathogenic mechanisms with altered methylation status are beginning to be elucidated. These findings are gradually translating into improved understanding of disease pathogenesis and clinical applications. Functional studies in osteoarthritis, rheumatoid arthritis, and SLE are now identifying downstream molecular alterations that may confer disease susceptibility. Epigenetic markers are being validated as prognostic and therapeutic disease biomarkers in sarcoma, and clinical trials of hypomethylating agents as treatments for sarcoma are being conducted. In concert with advances in throughput and cost-efficiency of available technologies, future epigenetic research will enable greater characterisation and treatment for both common and rare osteoarticular diseases.
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Affiliation(s)
- S B Roberts
- Bone Research Group, Centre for Genomics and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK,
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Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH, Roberts SB. Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas. BMC Genomics 2014; 15:951. [PMID: 25362893 PMCID: PMC4531390 DOI: 10.1186/1471-2164-15-951] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 10/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end-of-century open ocean pH reductions. In order to assess the impact of ocean acidification on marine invertebrates, Pacific oysters (Crassostrea gigas) were exposed to one of four different p CO2 levels for four weeks: 400 μatm (pH 8.0), 800 μatm (pH 7.7), 1000 μatm (pH 7.6), or 2800 μatm (pH 7.3). RESULTS At the end of the four week exposure period, oysters in all four p CO2 environments deposited new shell, but growth rate was not different among the treatments. However, micromechanical properties of the new shell were compromised by elevated p CO2. Elevated p CO2 affected neither whole body fatty acid composition, nor glycogen content, nor mortality rate associated with acute heat shock. Shotgun proteomics revealed that several physiological pathways were significantly affected by ocean acidification, including antioxidant response, carbohydrate metabolism, and transcription and translation. Additionally, the proteomic response to a second stress differed with p CO2, with numerous processes significantly affected by mechanical stimulation at high versus low p CO2 (all proteomics data are available in the ProteomeXchange under the identifier PXD000835). CONCLUSIONS Oyster physiology is significantly altered by exposure to elevated p CO2, indicating changes in energy resource use. This is especially apparent in the assessment of the effects of p CO2 on the proteomic response to a second stress. The altered stress response illustrates that ocean acidification may impact how oysters respond to other changes in their environment. These data contribute to an integrative view of the effects of ocean acidification on oysters as well as physiological trade-offs during environmental stress.
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Affiliation(s)
- Emma Timmins-Schiffman
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, USA.
| | - William D Coffey
- Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ, 08628, USA.
| | - Wilber Hua
- Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ, 08628, USA.
| | - Brook L Nunn
- Genome Sciences, University of Washington, Box 355065, Seattle, WA, 98195, USA.
| | - Gary H Dickinson
- Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ, 08628, USA.
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, USA.
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Deckersbach T, Das SK, Urban LE, Salinardi T, Batra P, Rodman AM, Arulpragasam AR, Dougherty DD, Roberts SB. Pilot randomized trial demonstrating reversal of obesity-related abnormalities in reward system responsivity to food cues with a behavioral intervention. Nutr Diabetes 2014; 4:e129. [PMID: 25177910 PMCID: PMC4183968 DOI: 10.1038/nutd.2014.26] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 06/27/2014] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES Obesity is associated with hyperactivation of the reward system for high-calorie (HC) versus low-calorie (LC) food cues, which encourages unhealthy food selection and overeating. However, the extent to which this hyperactivation can be reversed is uncertain, and to date there has been no demonstration of changes by behavioral intervention. SUBJECTS AND METHODS We used functional magnetic resonance imaging to measure changes in activation of the striatum for food images at baseline and 6 months in a pilot study of 13 overweight or obese adults randomized to a control group or a novel weight-loss intervention. RESULTS Compared to controls, intervention participants achieved significant weight loss (-6.3±1.0 kg versus +2.1±1.1 kg, P<0.001) and had increased activation for LC food images with a composition consistent with that recommended in the behavioral intervention at 6 months versus baseline in the right ventral putamen (P=0.04), decreased activation for HC images of typically consumed foods in the left dorsal putamen (P=0.01). There was also a large significant shift in relative activation favoring LC versus HC foods in both regions (P<0.04). CONCLUSIONS This study provides the first demonstration of a positive shift in activation of the reward system toward healthy versus unhealthy food cues in a behavioral intervention, suggesting new avenues to enhance behavioral treatments of obesity.
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Affiliation(s)
- T Deckersbach
- Division of Neurotherapeutics, Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - S K Das
- Energy Metabolism and Obesity Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - L E Urban
- Energy Metabolism and Obesity Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - T Salinardi
- Energy Metabolism and Obesity Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - P Batra
- Energy Metabolism and Obesity Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - A M Rodman
- Division of Neurotherapeutics, Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - A R Arulpragasam
- Division of Neurotherapeutics, Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - D D Dougherty
- Division of Neurotherapeutics, Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - S B Roberts
- Energy Metabolism and Obesity Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
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35
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Olson CE, Roberts SB. Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes. Front Physiol 2014; 5:224. [PMID: 24987376 PMCID: PMC4060414 DOI: 10.3389/fphys.2014.00224] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/28/2014] [Indexed: 01/21/2023] Open
Abstract
DNA methylation patterns and functions are variable across invertebrate taxa. In order to provide a better understanding of DNA methylation in the Pacific oyster (Crassostrea gigas), we characterized the genome-wide DNA methylation profile in male gamete cells using whole-genome bisulfite sequencing. RNA-Seq analysis was performed to examine the relationship between DNA methylation and transcript expression. Methylation status of over 7.6 million CpG dinucleotides was described with a majority of methylated regions occurring among intragenic regions. Overall, 15% of the CpG dinucleotides were determined to be methylated and the mitochondrial genome lacked DNA methylation. Integrative analysis of DNA methylation and RNA-Seq data revealed a positive association between methylation status, both in gene bodies and putative promoter regions, and expression. This study provides a comprehensive characterization of the distribution of DNA methylation in the oyster male gamete tissue and suggests that DNA methylation is involved in gene regulatory activity.
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Affiliation(s)
- Claire E Olson
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
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Abstract
The function of DNA methylation in species such as bivalves where the limited amount of DNA methylation is predominantly found in gene bodies remains unclear. An emerging possible explanation is that the role of gene body DNA methylation is dependent on gene function, a potential phenomenon that has arisen from selective pressure on lineage-specific life history traits. In genes contributing to phenotypes that benefit from increased plasticity, the absence of DNA methylation could contribute to stochastic transcriptional opportunities and increased transposable element activity. In genes where regulated control of activity is essential, DNA methylation may also play a role in targeted, predictable genome regulation. Here, we review the current knowledge concerning DNA methylation in bivalves and explore the putative role of DNA methylation in both an evolutionary and ecological context.
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37
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Gavery MR, Roberts SB. Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc. PeerJ 2013; 1:e215. [PMID: 24282674 PMCID: PMC3840415 DOI: 10.7717/peerj.215] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 11/01/2013] [Indexed: 12/18/2022] Open
Abstract
Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves.
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Affiliation(s)
- Mackenzie R Gavery
- School of Aquatic and Fishery Sciences, University of Washington , Seattle, WA , USA
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Storer CS, Quinn TP, Roberts SB. Quantitative PCR analysis used to characterize physiological changes in brain tissue of senescent sockeye salmon. Biogerontology 2013; 14:483-90. [PMID: 23948798 DOI: 10.1007/s10522-013-9448-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 07/24/2013] [Indexed: 11/24/2022]
Abstract
Senescence varies considerably among fishes, and understanding the evolutionary basis for this diversity has become an important area of study. For rapidly senescing species such as Pacific salmon, senescence is a complex process as these fish are initiating anorexia while migrating to natal spawning grounds, and die within days of reproduction. To better understand senescence in Pacific salmon we examined expression patterns for a suite of genes in brain tissue of pre-senescent and senescent sockeye salmon. Interestingly, a significant increase in expression of genes involved in telomere repair and immune activity was observed in senescent salmon. These data provide insight into physiological changes in salmon undergoing senescence and the factors contributing to variation in observed senescence rates among individuals and populations.
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Affiliation(s)
- C S Storer
- School of Aquatic and Fishery Sciences, University of Washington, 1122 Northeast Boat Street, P.O. Box 355020, Seattle, WA, 98195, USA,
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Timmins-Schiffman E, Nunn BL, Goodlett DR, Roberts SB. Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster. Conserv Physiol 2013; 1:cot009. [PMID: 27293593 PMCID: PMC4732435 DOI: 10.1093/conphys/cot009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/10/2013] [Accepted: 04/11/2013] [Indexed: 05/03/2023]
Abstract
Shotgun proteomics offers an efficient means to characterize proteins in a complex mixture, particularly when sufficient genomic resources are available. In order to assess the practical application of shotgun proteomics in the Pacific oyster (Crassostrea gigas), liquid chromatography coupled with tandem mass spectrometry was used to characterize the gill proteome. Using information from the recently published Pacific oyster genome, 1043 proteins were identified. Biological samples (n = 4) and corresponding technical replicates (three) were similar in both specific proteins identified and expression, as determined by normalized spectral abundance factor. A majority of the proteins identified (703) were present in all biological samples. Functional analysis of the protein repertoire illustrates that these proteins represent a wide range of biological processes, supporting the dynamic function of the gill. These insights are important for understanding environmental influences on the oyster, because the gill tissue acts as the interface between the oyster and its environment. In silico analysis indicated that this sequencing effort identified a large proportion of the complete gill proteome. Together, these data demonstrate that shotgun sequencing is a viable approach for biological discovery and will play an important role in future studies of oyster physiology.
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Affiliation(s)
- Emma Timmins-Schiffman
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA
| | - Brook L. Nunn
- Genomic Sciences, University of Washington, Box 355065, Seattle, WA 98195, USA
| | - David R. Goodlett
- Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195, USA
| | - Steven B. Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA
- Corresponding author: School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA. Tel: +1 206 685 3742.
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Timmins‐Schiffman EB, Friedman CS, Metzger DC, White SJ, Roberts SB. Genomic resource development for shellfish of conservation concern. Mol Ecol Resour 2012; 13:295-305. [DOI: 10.1111/1755-0998.12052] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/16/2012] [Accepted: 11/20/2012] [Indexed: 01/23/2023]
Affiliation(s)
| | - Carolyn S. Friedman
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
| | - Dave C. Metzger
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
| | - Samuel J. White
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
| | - Steven B. Roberts
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
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Storer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW, Seeb JE. Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism. PLoS One 2012; 7:e49018. [PMID: 23185290 PMCID: PMC3502385 DOI: 10.1371/journal.pone.0049018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 10/09/2012] [Indexed: 01/15/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.
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Affiliation(s)
- Caroline G. Storer
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Carita E. Pascal
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Steven B. Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - William D. Templin
- Gene Conservation Laboratory, Alaska Department of Fish and Game, Anchorage, Alaska, United States of America
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - James E. Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
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Roberts SB, Hauser L, Seeb LW, Seeb JE. Development of genomic resources for Pacific Herring through targeted transcriptome pyrosequencing. PLoS One 2012; 7:e30908. [PMID: 22383979 PMCID: PMC3288011 DOI: 10.1371/journal.pone.0030908] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 12/23/2011] [Indexed: 12/03/2022] Open
Abstract
Pacific herring (Clupea pallasii) support commercially and culturally important fisheries but have experienced significant additional pressure from a variety of anthropogenic and environmental sources. In order to provide genomic resources to facilitate organismal and population level research, high-throughput pyrosequencing (Roche 454) was carried out on transcriptome libraries from liver and testes samples taken in Prince William Sound, the Bering Sea, and the Gulf of Alaska. Over 40,000 contigs were identified with an average length of 728 bp. We describe an annotated transcriptome as well as a workflow for single nucleotide polymorphism (SNP) discovery and validation. A subset of 96 candidate SNPs chosen from 10,933 potential SNPs, were tested using a combination of Sanger sequencing and high-resolution melt-curve analysis. Five SNPs supported between-ocean-basin differentiation, while one SNP associated with immune function provided high differentiation between Prince William Sound and Kodiak Island within the Gulf of Alaska. These genomic resources provide a basis for environmental physiology studies and opportunities for marker development and subsequent population structure analysis.
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Affiliation(s)
- Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America.
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Roberts SB, Gavery MR. Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates? Front Physiol 2012; 2:116. [PMID: 22232607 PMCID: PMC3249382 DOI: 10.3389/fphys.2011.00116] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 12/14/2011] [Indexed: 11/13/2022] Open
Abstract
There is a significant amount of variation in DNA methylation characteristics across organisms. Likewise, the biological role of DNA methylation varies across taxonomic lineages. The complexity of DNA methylation patterns in invertebrates has only recently begun to be characterized in-depth. In some invertebrate species that have been examined to date, methylated DNA is found primarily within coding regions and patterning is closely associated with gene function. Here we provide a perspective on the potential role of DNA methylation in these invertebrates with a focus on how limited methylation may contribute to increased phenotypic plasticity in highly fluctuating environments. Specifically, limited methylation could facilitate a variety of transcriptional opportunities including access to alternative transcription start sites, increasing sequence mutations, exon skipping, and transient methylation.
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Affiliation(s)
- Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
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Gavery MR, Roberts SB. Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas. Comp Biochem Physiol Part D Genomics Proteomics 2011; 7:94-9. [PMID: 22244882 DOI: 10.1016/j.cbd.2011.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 12/16/2011] [Accepted: 12/20/2011] [Indexed: 12/21/2022]
Abstract
Advances in DNA sequencing technology have provided opportunities to produce new transcriptomic resources for species that lack completely sequenced genomes. However, there are limited examples that rely solely on ultra-short read sequencing technologies (e.g. Solexa, SOLiD) for transcript discovery and gene expression analysis (i.e. RNA-Seq). Here we use SOLiD sequencing to examine gene expression patterns in Pacific oyster (Crassostrea gigas) populations exposed to varying degrees of anthropogenic impact. Novel transcripts were identified and RNA-Seq analysis revealed several hundred differentially expressed genes. Gene enrichment analysis determined that in addition to biological processes predicted to be associated with anthropogenic influences (e.g. immune response), other processes play important roles including cell recognition and cell adhesion. To evaluate the effectiveness of restricting characterization solely to short read sequences, mapping and RNA-Seq analysis were also performed using publicly available transcriptome sequence data as a scaffold. This study demonstrates that ultra-short read sequencing technologies can effectively generate novel transcriptome information, identify differentially expressed genes, and will be important for examining environmental physiology of non-model organisms.
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Affiliation(s)
- Mackenzie R Gavery
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, WA 98105, USA.
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Roberts SB, Sunila I, Wikfors GH. Immune response and mechanical stress susceptibility in diseased oysters, Crassostrea virginica. J Comp Physiol B 2011; 182:41-8. [DOI: 10.1007/s00360-011-0605-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 07/05/2011] [Accepted: 07/28/2011] [Indexed: 11/28/2022]
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Seeb JE, Pascal CE, Grau ED, Seeb LW, Templin WD, Harkins T, Roberts SB. Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Mol Ecol Resour 2010; 11:335-48. [PMID: 21429141 DOI: 10.1111/j.1755-0998.2010.02936.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Until recently, single nucleotide polymorphism (SNP) discovery in nonmodel organisms faced many challenges, often depending upon a targeted-gene approach and Sanger sequencing of many individuals. The advent of next-generation sequencing technologies has dramatically improved discovery, but validating and testing SNPs for use in population studies remain labour intensive. Here, we detail a SNP discovery and validation pipeline that incorporates 454 pyrosequencing, high-resolution melt analysis (HRMA) and 5' nuclease genotyping. We generated 4.59×10(8) bp of redundant sequence from transcriptomes of two individual chum salmon, a highly valued species across the Pacific Rim. Nearly 26000 putative SNPs were identified--some as heterozygotes and some as homozygous for different nucleotides in the two individuals. For validation, we selected 202 templates containing single putative SNPs and conducted HRMA on 10 individuals from each of 19 populations from across the species range. Finally, 5' nuclease genotyping validated 37 SNPs that conformed to Hardy-Weinberg equilibrium expectations. Putative SNPs expressed as heterozygotes in an ascertainment individual had more than twice the validation rate of those homozygous for different alleles in the two fish, suggesting that many of the latter may have been paralogous sequence variants. Overall, this validation rate of 37/202 suggests that we have found more than 4500 templates containing SNPs for use in this population set. We anticipate using this pipeline to significantly expand the number of SNPs available for the studies of population structure and mixture analyses as well as for the studies of adaptive genetic variation in nonmodel organisms.
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Affiliation(s)
- J E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195-5020, USA
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Gavery MR, Roberts SB. DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas). BMC Genomics 2010; 11:483. [PMID: 20799955 PMCID: PMC2996979 DOI: 10.1186/1471-2164-11-483] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 08/27/2010] [Indexed: 12/18/2022] Open
Abstract
Background DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential functions of DNA methylation in the Pacific oyster (Crassostrea gigas). Results Methylation sensitive PCR and bisulfite sequencing PCR approaches were used to identify CpG methylation in C. gigas genes and demonstrated that this species possesses intragenic methylation. In silico analysis of CpGo/e ratios in publicly available sequence data suggests that DNA methylation is a common feature of the C. gigas genome, and that specific functional categories of genes have significantly different levels of methylation. Conclusions The Pacific oyster genome displays intragenic DNA methylation and contains genes necessary for DNA methylation in animals. Results of this investigation suggest that DNA methylation has regulatory functions in Crassostrea gigas, particularly in gene families that have inducible expression, including those involved in stress and environmental responses.
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Affiliation(s)
- Mackenzie R Gavery
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, Washington, USA
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Abstract
We report that the skin of cuttlefish, Sepia officinalis, contains opsin transcripts suggesting a possible role of distributed light sensing for dynamic camouflage and signalling. The mRNA coding for opsin from various body regions was amplified and sequenced, and gene expression was detected in fin and ventral skin samples. The amino acid sequence of the opsin polypeptide that these transcripts would produce was identical in retina and fin tissue samples, but the ventral skin opsin transcripts differed by a single amino acid. The diverse camouflage and signalling body patterns of cephalopods are visually controlled, and these findings suggest a possible additional mechanism of light sensing and subsequent skin patterning. Cuttlefish, along with a number of other cephalopod species, have been shown to be colour-blind. Since the opsin in the fin is identical to that of the retina (λmax=492 nm), and the ventral transcripts are also unlikely to be spectrally different, colour discrimination by the skin opsins is unlikely. However, spectral discrimination could be provided by involving other skin structures (chromatophores and iridophores), which produce changeable colours and patterns. This 'distributed sensing' could supplement the otherwise visually driven dynamic camouflage system by assisting with colour or brightness matching to adjacent substrates.
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Affiliation(s)
- Lydia M Mäthger
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
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Melanson KJ, Greenberg AS, Ludwig DS, Saltzman E, Dallal GE, Roberts SB. Blood glucose and hormonal responses to small and large meals in healthy young and older women. J Gerontol A Biol Sci Med Sci 2008; 53:B299-305. [PMID: 18314561 DOI: 10.1093/gerona/53a.4.b299] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Blood glucose regulation in the fasting and fed states has important implications for health. In addition, the ability to maintain normal blood glucose homeostasis may be an important determinant of an individual's capacity to regulate food intake. We tested the hypothesis that aging is associated with an impairment in the ability to maintain normal blood glucose homeostasis following the consumption of large meals but not small ones, a factor that could help to explain age-related impairments in the control of food intake and energy regulation. The subjects were eight healthy younger women (25 +/- 2 years, SD) and eight healthy older women (72 +/- 2 years) with normal body weight and glucose tolerance. Following a 36-h period when diet and physical activity were controlled, subjects consumed test meals containing 0, 1046, 2092, and 4184 kJ (simulating extended fasting, and consumption of a snack, a small meal, and a moderately large meal), with 35% of energy from fat, 48% from carbohydrate, and 17% from protein. Each subject consumed each of the test meals on a separate occasion. Serial blood samples were collected at baseline and during 5 h after consumption of the meals. Measurements were made of circulating glucose, insulin, glucagon, free fatty acids, and triglycerides. There was no significant difference between young and older women in their hormone and metabolite responses to fasting and consumption of the 1046-kJ meal. However, following consumption of 2092 and 4148 kJ, older individuals showed exaggerated responses and a delayed return to premeal values for glucose (p = .023), insulin (p = .010), triglycerides (p = .023), and the ratio of insulin to glucagon (p = .026). In conclusion, these results suggest an impairment in the hormonal and metabolite responses to large meals in older women.
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Affiliation(s)
- K J Melanson
- The Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA
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Gilhooly CH, Das SK, Golden JK, McCrory MA, Dallal GE, Saltzman E, Kramer FM, Roberts SB. Food cravings and energy regulation: the characteristics of craved foods and their relationship with eating behaviors and weight change during 6 months of dietary energy restriction. Int J Obes (Lond) 2007; 31:1849-58. [PMID: 17593902 DOI: 10.1038/sj.ijo.0803672] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To examine characteristics of craved foods in relation to dietary energy restriction (ER) with high (HG) and low glycemic load (LG) diets. DESIGN Assessments of food cravings before and during a randomized controlled trial of HG and LG diets provided for 6 months. SUBJECTS Thirty-two healthy, overweight women aged 20-42 years. MEASUREMENTS Self-reported food cravings and dietary intake, body weight, weight history and measures of eating behaviors. RESULTS Foods craved at baseline were more than twice as high in energy density as the habitual diet (3.7+/-1.5 vs 1.7+/-0.3 kcal/g; P<0.001), and on average were lower in protein (P<0.001) and fiber (P<0.001) and higher in fat (P=0.002). There were no statistically significant changes in nutritional characteristics of craved foods after 6 months of ER. There was a significant relationship between reported portion size of craved food consumed at baseline and lifetime high body mass index (r=0.49, P=0.005). Additionally, there was a significant association between susceptibility to hunger and craving frequency at baseline, and there were significant relationships between hunger score, craving frequency, strength and percentage of time that cravings are given in to after 6 months of ER. In multiple regression models, subjects who lost a greater percentage of weight craved higher energy-dense foods at month 6 of ER, but also reported giving in to food cravings less frequently (adjusted R (2)=0.31, P=0.009). CONCLUSION High energy density and fat content, and low protein and fiber contents were identifying characteristics of craved foods. The relationships between craving variables and hunger score suggest that the relative influence of hunger susceptibility on cravings may be important before and especially after ER. Portion size of craved foods and frequency of giving in to food cravings appear to be important areas for focus in lifestyle modification programs for long-term weight loss.
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Affiliation(s)
- C H Gilhooly
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA
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